Variant report

Variant	rs17111419
Chromosome Location	chr1:94791006-94791007
allele	A/G
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	SIN3AK20	chr1:94790957-94791765	MCF-7	breast:	n/a	n/a
2	FOXM1	chr1:94790538-94792201	ECC-1	luminal epithelium:	n/a	n/a
3	SP1	chr1:94790546-94792480	HCT-116	colon:	n/a	chr1:94791610-94791624 chr1:94791610-94791620 chr1:94791611-94791620
4	EP300	chr1:94790776-94791808	SK-N-SH_RA	brain:	n/a	n/a
5	PBX3	chr1:94790706-94792426	SK-N-SH	brain:	n/a	n/a
6	NR3C1	chr1:94790798-94791125	A549	lung:	n/a	n/a
7	TCF12	chr1:94790611-94792143	A549	lung:	n/a	chr1:94791961-94791970
8	NR3C1	chr1:94790780-94791511	A549	lung:	n/a	chr1:94791388-94791395
9	FOS	chr1:94790940-94791803	MCF10A-Er-Src	breast:	n/a	chr1:94791573-94791580 chr1:94791292-94791303
10	TCF7L2	chr1:94790876-94791553	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:94788372-94793300	HUVEC	blood vessel:	n/a	n/a
12	FOXA2	chr1:94790990-94791879	A549	lung:	n/a	n/a
13	EP300	chr1:94790696-94791081	SK-N-SH_RA	brain:	n/a	n/a
14	GATA3	chr1:94790702-94792121	A549	lung:	n/a	chr1:94792041-94792048 chr1:94792034-94792055 chr1:94792041-94792048 chr1:94792036-94792052 chr1:94792041-94792048
15	FOS	chr1:94790963-94791785	MCF10A-Er-Src	breast:	n/a	chr1:94791573-94791580 chr1:94791292-94791303
16	GATA2	chr1:94790825-94791804	HUVEC	blood vessel:	n/a	n/a
17	SIN3AK20	chr1:94790652-94792035	HCT-116	colon:	n/a	n/a
18	FOSL2	chr1:94790748-94791926	A549	lung:	n/a	chr1:94791573-94791580
19	NFIC	chr1:94790613-94792283	ECC-1	luminal epithelium:	n/a	chr1:94791323-94791351
20	RAD21	chr1:94790828-94791902	ECC-1	luminal epithelium:	n/a	n/a
21	NFIC	chr1:94790796-94791933	SK-N-SH	brain:	n/a	chr1:94791323-94791351
22	JUND	chr1:94790781-94792261	HCT-116	colon:	n/a	chr1:94791573-94791580
23	NR3C1	chr1:94790797-94791141	ECC-1	luminal epithelium:	n/a	n/a
24	RFX5	chr1:94790836-94792158	Hela-S3	cervix:	n/a	n/a
25	JUND	chr1:94790953-94792383	SK-N-SH	brain:	n/a	chr1:94791573-94791580
26	STAT3	chr1:94790926-94791660	Hela-S3	cervix:	n/a	chr1:94791270-94791281
27	MYC	chr1:94790953-94791759	MCF10A-Er-Src	breast:	n/a	n/a
28	RXRA	chr1:94790819-94791940	SK-N-SH	brain:	n/a	n/a
29	MAX	chr1:94790788-94792302	SK-N-SH	brain:	n/a	n/a
30	EP300	chr1:94790896-94792175	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:94790999-94791160	ProgFib	skin:	n/a	n/a
32	CEBPB	chr1:94790842-94791859	A549	lung:	n/a	n/a
33	POLR2A	chr1:94790952-94791007	HUVEC	blood vessel:	n/a	n/a
34	PBX3	chr1:94790749-94792357	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr1:94790793-94791449	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr1:94790968-94791765	MCF10A-Er-Src	breast:	n/a	chr1:94791573-94791580 chr1:94791292-94791303
37	NFIC	chr1:94790496-94792356	ECC-1	luminal epithelium:	n/a	chr1:94791323-94791351
38	POLR2A	chr1:94790757-94791835	SK-N-SH	brain:	n/a	n/a
39	FOXM1	chr1:94790740-94792222	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr1:94790736-94792332	PANC-1	pancreas:	n/a	n/a
41	ZBTB33	chr1:94791001-94791862	SK-N-SH	brain:	n/a	n/a
42	SRF	chr1:94790963-94791892	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr1:94790783-94791453	HCT-116	colon:	n/a	n/a
44	EP300	chr1:94790848-94792241	Hela-S3	cervix:	n/a	n/a
45	JUND	chr1:94790836-94792379	Hela-S3	cervix:	n/a	chr1:94791573-94791580
46	POLR2A	chr1:94790776-94793338	PANC-1	pancreas:	n/a	n/a
47	GATA3	chr1:94790751-94792409	SK-N-SH	brain:	n/a	chr1:94792041-94792048 chr1:94792034-94792055 chr1:94792041-94792048 chr1:94792036-94792052 chr1:94792041-94792048
48	MAX	chr1:94790899-94791679	Hela-S3	cervix:	n/a	n/a
49	TFAP2A	chr1:94790867-94791522	Hela-S3	cervix:	n/a	chr1:94791304-94791319
50	TEAD4	chr1:94790865-94792065	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236098	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1054626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165103	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11165114	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12022859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12024941	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12027548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12031606	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12036085	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038745	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12039546	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12042509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12046536	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12093742	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12562103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12563826	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360365	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1576592	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1611832	0.94[EUR][1000 genomes]
rs1622451	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623248	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1629275	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1687947	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1687950	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17111408	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17111426	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17111436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1765636	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1765640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1929131	0.86[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1999270	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1999271	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2130899	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391472	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35275815	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789690	0.83[EUR][1000 genomes]
rs4543802	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847201	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847296	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55961421	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56037795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57666908	0.83[EUR][1000 genomes]
rs6541343	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6541345	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6662877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6673491	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6675959	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681827	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66918029	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66961454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67180557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67554381	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67612304	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67681803	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67807923	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68193246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7413345	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7415246	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515965	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7520754	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525320	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7533977	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7554714	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94783200-94792800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:94784800-94791400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:94785400-94792000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94785600-94792200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94785800-94791200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94785800-94791600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:94785800-94791800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:94787200-94791400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:94787200-94791400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:94787200-94795200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:94787800-94793400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:94788400-94791400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:94788400-94792000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:94788400-94792600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:94788400-94794000	Enhancers	NHLF	lung
16	chr1:94788600-94792000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:94788600-94792000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:94788600-94792000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:94788600-94792000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:94788600-94800800	Weak transcription	Pancreas	Pancrea
21	chr1:94788800-94792000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:94789000-94792800	Enhancers	Fetal Kidney	kidney
23	chr1:94789400-94791200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:94789400-94792000	Enhancers	HSMM	muscle
25	chr1:94789800-94791200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:94789800-94793000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:94790200-94792400	Enhancers	NHDF-Ad	bronchial
28	chr1:94790200-94796000	Enhancers	HMEC	breast
29	chr1:94790400-94791200	Enhancers	Psoas Muscle	Psoas
30	chr1:94790400-94791200	Enhancers	Spleen	Spleen
31	chr1:94790400-94791400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:94790400-94793200	Enhancers	Fetal Muscle Leg	muscle
33	chr1:94790400-94793400	Enhancers	Placenta	Placenta
34	chr1:94790400-94793800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:94790600-94792600	Enhancers	NH-A	brain
36	chr1:94790600-94792800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:94790800-94791200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:94790800-94791200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:94790800-94791200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:94790800-94791200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:94790800-94791200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:94790800-94791200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:94790800-94791200	Enhancers	Aorta	Aorta
44	chr1:94790800-94791200	Enhancers	Right Atrium	heart
45	chr1:94790800-94791200	Flanking Active TSS	A549	lung
46	chr1:94790800-94791200	Flanking Active TSS	HUVEC	blood vessel
47	chr1:94790800-94791200	Flanking Active TSS	NHEK	skin
48	chr1:94790800-94791200	Flanking Active TSS	Osteobl	bone
49	chr1:94790800-94791400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:94790800-94791400	Flanking Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links