Variant report

Variant	rs3827531
Chromosome Location	chr1:159902526-159902527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:159902520-159902670	HPAF	blood vessel:	n/a	n/a
2	CTCF	chr1:159902520-159902670	HRE	kidney:	n/a	n/a
3	NFIC	chr1:159902428-159902975	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr1:159902418-159902980	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr1:159902520-159902670	GM12871	blood:	n/a	n/a
6	CTCF	chr1:159902500-159902650	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr1:159902500-159902650	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159899215..159903293-chr1:159903611..159908278,6	MCF-7	breast:

Variant related genes	Relation type
IGSF9	TF binding region
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13052	0.92[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7543462	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv464150	chr1:159860917-159908393	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv548052	chr1:159860917-159908393	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv548053	chr1:159885500-159908393	Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv516637	chr1:159889686-159908393	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	62 gene(s)	inside rSNPs	diseases
8	nsv548054	chr1:159895979-159907441	Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159895800-159906600	Weak transcription	Small Intestine	intestine
2	chr1:159896000-159906000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:159896200-159906000	Genic enhancers	Fetal Intestine Small	intestine
4	chr1:159896400-159906000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:159896400-159906000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:159896400-159906600	Weak transcription	Right Atrium	heart
7	chr1:159896600-159906000	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr1:159896600-159906000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:159896600-159907200	Weak transcription	Fetal Heart	heart
10	chr1:159896600-159908600	Weak transcription	Fetal Kidney	kidney
11	chr1:159897000-159906200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:159897000-159906200	Strong transcription	Fetal Brain Female	brain
13	chr1:159897200-159902600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:159897400-159905400	Strong transcription	Liver	Liver
15	chr1:159897800-159906400	Weak transcription	Fetal Brain Male	brain
16	chr1:159898000-159906000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:159898000-159906000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:159898200-159902600	Weak transcription	GM12878-XiMat	blood
19	chr1:159898200-159905800	Weak transcription	A549	lung
20	chr1:159899200-159906000	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:159899400-159906200	Weak transcription	Gastric	stomach
22	chr1:159899400-159906400	Strong transcription	Fetal Stomach	stomach
23	chr1:159899600-159902600	Strong transcription	Colonic Mucosa	Colon
24	chr1:159899800-159902600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:159899800-159905400	Weak transcription	Stomach Mucosa	stomach
26	chr1:159899800-159905800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:159899800-159906000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:159900000-159906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:159900200-159902800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:159900200-159906000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:159900600-159905600	Strong transcription	Fetal Intestine Large	intestine
32	chr1:159900800-159905800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:159901200-159904400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:159901400-159903400	Weak transcription	Fetal Thymus	thymus
35	chr1:159901400-159903800	Enhancers	Esophagus	oesophagus
36	chr1:159901600-159904000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:159901600-159904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:159901600-159905000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:159901800-159903000	Enhancers	NHEK	skin
40	chr1:159901800-159904000	Enhancers	HMEC	breast
41	chr1:159902000-159903000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:159902000-159903000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:159902200-159902800	Enhancers	Lung	lung
44	chr1:159902200-159903000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:159902200-159903800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:159902200-159904400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:159902400-159902800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:159902400-159902800	Enhancers	Fetal Muscle Trunk	muscle
49	chr1:159902400-159903000	Enhancers	Spleen	Spleen
50	chr1:159902400-159903800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links