Variant report

Variant	rs6674562
Chromosome Location	chr1:146624487-146624488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:146555134..146556670-chr1:146623816..146625708,2	K562	blood:
2	chr1:146623016..146624797-chr1:146633166..146635913,3	MCF-7	breast:
3	chr1:146578104..146580679-chr1:146623969..146626202,2	MCF-7	breast:
4	chr1:146554825..146557701-chr1:146623843..146627168,3	MCF-7	breast:
5	chr1:146622097..146624965-chr1:146629211..146630728,2	K562	blood:
6	chr1:146623510..146625059-chr1:146626745..146629134,2	K562	blood:
7	chr1:146610691..146613596-chr1:146624055..146626822,2	MCF-7	breast:
8	chr1:146618023..146620709-chr1:146623183..146625332,2	K562	blood:
9	chr1:146623231..146625230-chr1:146632518..146634098,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230832	Chromatin interaction
ENSG00000131791	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10159076	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10900319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900331	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11239952	0.82[ASN][1000 genomes]
rs11239953	0.86[JPT][hapmap]
rs11239956	0.86[JPT][hapmap]
rs12023638	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023644	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12024575	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12027580	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12029358	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030403	1.00[EUR][1000 genomes]
rs12031124	1.00[EUR][1000 genomes]
rs12031956	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12032300	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12032578	1.00[EUR][1000 genomes]
rs12036480	1.00[EUR][1000 genomes]
rs12037324	0.86[ASN][1000 genomes]
rs12038539	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12039254	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12039364	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12039400	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12040321	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12044706	0.89[CHB][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12047915	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12049109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12736102	0.85[JPT][hapmap]
rs13375602	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1932978	0.86[JPT][hapmap]
rs2297751	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3766521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56854335	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59801063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6593750	0.86[JPT][hapmap]
rs6593752	0.86[JPT][hapmap]
rs6593766	1.00[EUR][1000 genomes]
rs6655945	0.89[ASN][1000 genomes]
rs6657665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6681716	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6690158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696488	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72708581	0.91[ASN][1000 genomes]
rs74119821	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74122342	1.00[EUR][1000 genomes]
rs7512450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519377	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7519804	0.86[JPT][hapmap]
rs7521301	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9988435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146616800-146625200	Weak transcription	Pancreas	Pancrea
2	chr1:146617000-146624800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:146618600-146625400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:146618800-146628800	Weak transcription	Lung	lung
5	chr1:146618800-146628800	Weak transcription	Spleen	Spleen
6	chr1:146619200-146630600	Weak transcription	Gastric	stomach
7	chr1:146619800-146625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:146619800-146628000	Weak transcription	HSMMtube	muscle
9	chr1:146621200-146625800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:146621600-146624600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:146621600-146624800	Weak transcription	Primary B cells from cord blood	blood
12	chr1:146621600-146629400	Weak transcription	NHDF-Ad	bronchial
13	chr1:146622200-146625400	Weak transcription	Aorta	Aorta
14	chr1:146622200-146627200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:146622400-146625400	Weak transcription	Ovary	ovary
16	chr1:146622400-146628000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:146622600-146625200	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:146622800-146624800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:146622800-146625000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:146622800-146625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:146622800-146625000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:146622800-146625200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:146622800-146625800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:146622800-146630000	Weak transcription	Small Intestine	intestine
25	chr1:146623000-146624600	Weak transcription	Primary T cells from cord blood	blood
26	chr1:146623000-146624600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:146623000-146625200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:146623000-146625200	Weak transcription	Brain Germinal Matrix	brain
29	chr1:146623000-146625400	Weak transcription	NH-A	brain
30	chr1:146623000-146625600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:146623000-146625800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:146623000-146627000	Weak transcription	Fetal Intestine Large	intestine
33	chr1:146623000-146628800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:146623200-146624800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:146623200-146625200	Weak transcription	HSMM	muscle
36	chr1:146623200-146625200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:146623200-146625800	Weak transcription	HMEC	breast
38	chr1:146623200-146626200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:146623200-146629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:146623200-146629200	Weak transcription	Brain Angular Gyrus	brain
41	chr1:146623200-146629400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:146623200-146629600	Weak transcription	Fetal Brain Male	brain
43	chr1:146623400-146625000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:146623400-146625000	Weak transcription	Adipose Nuclei	Adipose
45	chr1:146623400-146625200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:146623400-146625200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:146623400-146625200	Weak transcription	Psoas Muscle	Psoas
48	chr1:146623400-146625200	Weak transcription	Osteobl	bone
49	chr1:146623400-146625400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:146623400-146625600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links