Variant report

Variant	rs10443176
Chromosome Location	chr1:77686646-77686647
allele	A/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	STAT3	chr1:77686416-77686803	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:77686415-77686673	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr1:77686303-77686696	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:77686365-77686777	Hela-S3	cervix:	n/a	n/a
5	FOS	chr1:77686417-77686808	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:77686393-77686803	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr1:77686262-77686762	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:77686415-77686810	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr1:77686337-77686744	IMR90	lung:	n/a	n/a
10	STAT3	chr1:77686350-77686801	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr1:77686413-77686747	A549	lung:	n/a	n/a
12	STAT3	chr1:77686391-77686830	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:77686298-77686827	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:77686353-77686833	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AK5-1	chr1:77686609-77686678	XLOC_000263
2	lnc-AK5-1	chr1:77686473-77686671	XLOC_000263
3	lnc-AK5-1	chr1:77686286-77690011	NONHSAT004022

Variant related genes	Relation type
PIGK	TF binding region
ENSG00000154027	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1010061	1.00[ASN][1000 genomes]
rs10518445	1.00[ASN][1000 genomes]
rs11162275	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162284	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162287	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576574	1.00[ASN][1000 genomes]
rs12077763	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090495	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119019	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120921	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122553	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12123535	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126662	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143529	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562335	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1305486	1.00[ASN][1000 genomes]
rs1502525	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100100	1.00[ASN][1000 genomes]
rs17100141	1.00[ASN][1000 genomes]
rs17100143	1.00[ASN][1000 genomes]
rs17100304	1.00[ASN][1000 genomes]
rs17368950	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827448	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993266	1.00[ASN][1000 genomes]
rs2004962	1.00[ASN][1000 genomes]
rs41292260	1.00[ASN][1000 genomes]
rs41292264	1.00[ASN][1000 genomes]
rs4949772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949773	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949778	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56666939	1.00[ASN][1000 genomes]
rs57267651	1.00[ASN][1000 genomes]
rs57389685	1.00[ASN][1000 genomes]
rs60792794	1.00[ASN][1000 genomes]
rs61782906	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603937	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696605	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683932	1.00[ASN][1000 genomes]
rs72944757	1.00[ASN][1000 genomes]
rs73002568	1.00[ASN][1000 genomes]
rs73004429	1.00[ASN][1000 genomes]
rs73004430	1.00[ASN][1000 genomes]
rs73004434	1.00[ASN][1000 genomes]
rs7519485	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544099	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550325	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77684600-77686800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:77685200-77687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:77685200-77687800	Weak transcription	Spleen	Spleen
4	chr1:77685400-77688000	Weak transcription	Gastric	stomach
5	chr1:77685400-77689600	Weak transcription	Esophagus	oesophagus
6	chr1:77685600-77693400	Weak transcription	Pancreas	Pancrea
7	chr1:77685800-77686800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:77685800-77687600	Weak transcription	Fetal Stomach	stomach
9	chr1:77685800-77687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:77685800-77687800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:77685800-77687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:77685800-77687800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:77685800-77687800	Weak transcription	Aorta	Aorta
14	chr1:77685800-77688400	Weak transcription	Right Atrium	heart
15	chr1:77685800-77688600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:77685800-77688600	Weak transcription	Fetal Thymus	thymus
17	chr1:77685800-77688600	Weak transcription	Psoas Muscle	Psoas
18	chr1:77685800-77688800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:77685800-77689000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:77685800-77689600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:77685800-77689600	Weak transcription	Ovary	ovary
22	chr1:77685800-77690000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:77685800-77692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:77685800-77695600	Weak transcription	Left Ventricle	heart
25	chr1:77686000-77686800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:77686000-77686800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:77686000-77686800	Enhancers	NH-A	brain
28	chr1:77686000-77687000	Enhancers	Brain Substantia Nigra	brain
29	chr1:77686000-77687400	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:77686000-77687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:77686000-77688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:77686000-77688000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:77686000-77688000	Weak transcription	Fetal Intestine Large	intestine
34	chr1:77686000-77688000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:77686000-77688600	Weak transcription	Fetal Brain Female	brain
36	chr1:77686000-77688600	Weak transcription	Right Ventricle	heart
37	chr1:77686000-77689000	Weak transcription	HSMM	muscle
38	chr1:77686000-77689600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:77686000-77689600	Weak transcription	Thymus	Thymus
40	chr1:77686000-77690600	Weak transcription	Primary B cells from cord blood	blood
41	chr1:77686000-77690800	Weak transcription	Fetal Brain Male	brain
42	chr1:77686000-77691600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:77686000-77692200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:77686000-77692400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:77686000-77694600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:77686000-77694600	Weak transcription	Fetal Kidney	kidney
47	chr1:77686000-77699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:77686200-77686800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:77686200-77686800	Enhancers	HMEC	breast
50	chr1:77686200-77687000	Enhancers	NHDF-Ad	bronchial

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