Variant report

Variant	rs3753427
Chromosome Location	chr1:147140454-147140455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:147117692..147123079-chr1:147140177..147144336,6	MCF-7	breast:
2	chr1:147104502..147107147-chr1:147139183..147141986,2	MCF-7	breast:
3	chr1:147125294..147131165-chr1:147136519..147143336,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162836	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12119687	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12122273	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124583	0.92[ASN][1000 genomes]
rs3766505	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4950467	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4950469	0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs61809196	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66792067	0.82[ASN][1000 genomes]
rs6686414	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539271	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv872266	chr1:147020099-147381558	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
21	nsv831426	chr1:147089930-147265267	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147113000-147141400	Weak transcription	Fetal Brain Male	brain
2	chr1:147114000-147141000	Weak transcription	Osteobl	bone
3	chr1:147120000-147141400	Weak transcription	Fetal Thymus	thymus
4	chr1:147122000-147141400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:147122400-147141600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:147124200-147141200	Weak transcription	Psoas Muscle	Psoas
7	chr1:147124400-147141000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:147124400-147141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:147124400-147141400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:147124600-147141000	Weak transcription	A549	lung
11	chr1:147127000-147140800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:147127200-147140800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:147127400-147140800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:147127400-147141200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:147127400-147141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:147127400-147141400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:147127800-147141000	Weak transcription	Small Intestine	intestine
18	chr1:147127800-147141600	Weak transcription	Placenta	Placenta
19	chr1:147128600-147141600	Weak transcription	Lung	lung
20	chr1:147128800-147141400	Weak transcription	Esophagus	oesophagus
21	chr1:147130600-147140800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:147130600-147141000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:147130800-147141400	Weak transcription	Right Ventricle	heart
24	chr1:147130800-147141400	Weak transcription	HSMMtube	muscle
25	chr1:147131000-147140800	Weak transcription	Hela-S3	cervix
26	chr1:147131000-147141000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:147131000-147141000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:147131000-147141000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:147131000-147141000	Weak transcription	Brain Substantia Nigra	brain
30	chr1:147131000-147141000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:147131000-147141400	Weak transcription	Colonic Mucosa	Colon
32	chr1:147131200-147140800	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:147131200-147141200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:147131600-147140800	Weak transcription	Primary T cells from cord blood	blood
35	chr1:147131600-147140800	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:147131600-147140800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:147131600-147140800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:147131600-147141200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:147131600-147141400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:147131600-147141400	Weak transcription	Adipose Nuclei	Adipose
41	chr1:147131600-147141400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:147131600-147141400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:147131600-147141400	Weak transcription	Gastric	stomach
44	chr1:147131600-147141400	Weak transcription	Ovary	ovary
45	chr1:147131600-147141400	Weak transcription	Pancreas	Pancrea
46	chr1:147131800-147140800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:147131800-147140800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:147131800-147141000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:147131800-147141000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:147131800-147141000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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