Variant report

Variant	rs12039400
Chromosome Location	chr1:146695327-146695328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146644917..146647495-chr1:146694467..146696944,2	K562	blood:
2	chr1:146642791..146647744-chr1:146694916..146698486,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1L-2	chr1:146695146-146695940	NONHSAT006006

Variant related genes	Relation type
ENSG00000131791	Chromatin interaction
ENSG00000271721	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000237188	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10159076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10900319	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10900331	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11239952	0.96[ASN][1000 genomes]
rs11239953	0.86[JPT][hapmap]
rs11239956	0.86[JPT][hapmap]
rs12023167	0.80[ASN][1000 genomes]
rs12023638	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12023644	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12024575	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12026060	0.80[ASN][1000 genomes]
rs12027580	0.95[ASN][1000 genomes]
rs12029358	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12031124	0.87[ASN][1000 genomes]
rs12031956	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12032300	0.89[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs12036480	0.91[ASN][1000 genomes]
rs12037324	1.00[ASN][1000 genomes]
rs12038539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[ASN][1000 genomes]
rs12038739	0.80[ASN][1000 genomes]
rs12039254	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12039364	0.96[ASN][1000 genomes]
rs12040321	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12041474	0.80[ASN][1000 genomes]
rs12044706	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12047915	0.98[ASN][1000 genomes]
rs12049109	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12239222	0.80[ASN][1000 genomes]
rs12565670	0.85[JPT][hapmap]
rs12736102	0.84[JPT][hapmap]
rs13375602	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1932978	0.86[JPT][hapmap]
rs2297751	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2297754	1.00[MEX][hapmap]
rs3766521	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[ASN][1000 genomes]
rs59801063	0.86[ASN][1000 genomes]
rs6593750	0.86[JPT][hapmap]
rs6593752	0.86[JPT][hapmap]
rs6593766	0.89[ASN][1000 genomes]
rs6655945	0.97[ASN][1000 genomes]
rs6657665	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6674562	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6681716	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6690158	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs6694020	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6696488	0.96[ASN][1000 genomes]
rs72708581	0.95[ASN][1000 genomes]
rs74122342	0.87[ASN][1000 genomes]
rs7512450	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7519377	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7519804	0.85[JPT][hapmap]
rs7521301	0.96[ASN][1000 genomes]
rs9988435	0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
4	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
7	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
8	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
10	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
15	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
16	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
21	nsv872257	chr1:146643555-146724923	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
23	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
25	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
26	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
27	nsv872258	chr1:146662018-146709784	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
28	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
29	nsv872259	chr1:146688941-146724923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
30	nsv946304	chr1:146695116-146696674	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146649800-146695400	Weak transcription	Left Ventricle	heart
2	chr1:146658800-146695400	Weak transcription	Lung	lung
3	chr1:146672800-146696400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:146674200-146696600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:146674400-146695400	Weak transcription	Right Ventricle	heart
6	chr1:146676800-146696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:146678400-146696200	Weak transcription	Colonic Mucosa	Colon
8	chr1:146679800-146696600	Weak transcription	Primary T cells from cord blood	blood
9	chr1:146680600-146696400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:146681200-146696400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:146681800-146696400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:146682800-146695400	Weak transcription	Spleen	Spleen
13	chr1:146683800-146696400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:146684000-146695400	Weak transcription	Small Intestine	intestine
15	chr1:146684000-146696400	Weak transcription	Adipose Nuclei	Adipose
16	chr1:146685200-146696600	Weak transcription	Aorta	Aorta
17	chr1:146686600-146696400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:146687000-146695600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:146687200-146696400	Weak transcription	Primary B cells from cord blood	blood
20	chr1:146687200-146696400	Weak transcription	Fetal Intestine Large	intestine
21	chr1:146687400-146696400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:146687600-146695400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:146688000-146696400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:146688400-146695400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:146690800-146696400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:146691200-146695400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:146692200-146696400	Weak transcription	Fetal Kidney	kidney
28	chr1:146693600-146695600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:146694400-146695400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr1:146694400-146695800	Flanking Active TSS	Liver	Liver
31	chr1:146694400-146695800	Enhancers	Brain Substantia Nigra	brain
32	chr1:146694800-146695400	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:146694800-146695600	Flanking Active TSS	Stomach Mucosa	stomach
34	chr1:146694800-146696000	Enhancers	Fetal Lung	lung
35	chr1:146694800-146696400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:146695000-146695800	Enhancers	Fetal Stomach	stomach
37	chr1:146695000-146696400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:146695200-146695400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr1:146695200-146695400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr1:146695200-146695400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:146695200-146695400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr1:146695200-146695400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr1:146695200-146695400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:146695200-146695400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:146695200-146695400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr1:146695200-146695400	Flanking Active TSS	Pancreas	Pancrea
47	chr1:146695200-146695400	Enhancers	Right Atrium	heart
48	chr1:146695200-146695400	Active TSS	HepG2	liver
49	chr1:146695200-146695600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:146695200-146695800	Flanking Active TSS	Gastric	stomach

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