Variant report

Variant	rs17111426
Chromosome Location	chr1:94792424-94792425
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	SP1	chr1:94790546-94792480	HCT-116	colon:	n/a	chr1:94791610-94791624 chr1:94791610-94791620 chr1:94791611-94791620
2	PBX3	chr1:94790706-94792426	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:94788372-94793300	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:94792358-94793426	HUVEC	blood vessel:	n/a	n/a
5	KAP1	chr1:94791872-94793277	HEK293	kidney:	n/a	chr1:94793114-94793122
6	POLR2A	chr1:94790776-94793338	PANC-1	pancreas:	n/a	n/a
7	MAFK	chr1:94792298-94792567	HepG2	liver:	n/a	chr1:94792436-94792452
8	GATA2	chr1:94792013-94793571	HUVEC	blood vessel:	n/a	chr1:94793265-94793272 chr1:94792041-94792048 chr1:94792034-94792055 chr1:94792041-94792048 chr1:94793263-94793273 chr1:94793265-94793272 chr1:94792036-94792052 chr1:94793258-94793279 chr1:94793265-94793272 chr1:94792041-94792048 chr1:94793260-94793276 chr1:94792470-94792478 chr1:94793262-94793274
9	POLR2A	chr1:94791959-94793256	HCT-116	colon:	n/a	n/a
10	TEAD4	chr1:94790762-94793483	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr1:94790580-94792430	SK-N-SH	brain:	n/a	chr1:94792263-94792271 chr1:94791961-94791970
12	BRCA1	chr1:94790819-94792500	Hela-S3	cervix:	n/a	n/a
13	JUND	chr1:94790681-94792438	HCT-116	colon:	n/a	chr1:94791573-94791580
14	TCF7L2	chr1:94790891-94792546	PANC-1	pancreas:	n/a	n/a
15	TCF12	chr1:94790698-94792457	SK-N-SH	brain:	n/a	chr1:94792263-94792271 chr1:94791961-94791970
16	GATA3	chr1:94790583-94792432	SK-N-SH	brain:	n/a	chr1:94792041-94792048 chr1:94792034-94792055 chr1:94792041-94792048 chr1:94792036-94792052 chr1:94792041-94792048

Variant related genes	Relation type
ENSG00000236098	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1054626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165103	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165114	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022859	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12024941	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12026367	0.93[AFR][1000 genomes]
rs12027548	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031606	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12036085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038745	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12039546	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046536	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12093742	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562103	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12563826	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360365	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1576592	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1611832	0.94[EUR][1000 genomes]
rs1622451	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1623248	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1623314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629275	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1687947	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1687950	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17111408	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111419	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];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1765636	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1765640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1929131	0.86[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1999270	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1999271	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130899	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391472	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35275815	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789690	0.83[EUR][1000 genomes]
rs4543802	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847201	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847296	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55961421	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56037795	0.95[AFR][1000 genomes];0.97[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];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6541345	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662877	0.97[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];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6675959	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6681827	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66918029	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66961454	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67180557	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67554381	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67612304	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67681803	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67807923	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68193246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7413345	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7415246	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515965	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7520754	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7525320	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533977	0.91[EUR][1000 genomes];0.86[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];0.86[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:80 , 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	chr1:94787200-94795200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:94787800-94793400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:94788400-94792600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:94788400-94794000	Enhancers	NHLF	lung
6	chr1:94788600-94800800	Weak transcription	Pancreas	Pancrea
7	chr1:94789000-94792800	Enhancers	Fetal Kidney	kidney
8	chr1:94789800-94793000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:94790200-94796000	Enhancers	HMEC	breast
10	chr1:94790400-94793200	Enhancers	Fetal Muscle Leg	muscle
11	chr1:94790400-94793400	Enhancers	Placenta	Placenta
12	chr1:94790400-94793800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:94790600-94792600	Enhancers	NH-A	brain
14	chr1:94790600-94792800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:94790800-94792800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:94790800-94793000	Enhancers	Stomach Mucosa	stomach
17	chr1:94790800-94793400	Enhancers	Fetal Stomach	stomach
18	chr1:94790800-94793600	Enhancers	Fetal Lung	lung
19	chr1:94790800-94799200	Enhancers	Fetal Heart	heart
20	chr1:94791000-94792600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:94791000-94792600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:94791000-94792800	Enhancers	Adipose Nuclei	Adipose
23	chr1:94791000-94792800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:94791000-94793000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:94791000-94793000	Enhancers	HepG2	liver
26	chr1:94791000-94793200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:94791200-94792800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:94791200-94792800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:94791200-94792800	Weak transcription	Ovary	ovary
30	chr1:94791200-94792800	Weak transcription	Right Atrium	heart
31	chr1:94791200-94793200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:94791200-94793400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:94791200-94793400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:94791200-94793400	Enhancers	Colon Smooth Muscle	Colon
35	chr1:94791200-94793800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:94791200-94793800	Enhancers	NHEK	skin
37	chr1:94791200-94795800	Weak transcription	Right Ventricle	heart
38	chr1:94791200-94796600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:94791200-94798600	Weak transcription	Lung	lung
40	chr1:94791400-94792600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:94791400-94792600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr1:94791400-94792800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:94791400-94792800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:94791800-94792800	Flanking Active TSS	A549	lung
45	chr1:94791800-94793400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:94791800-94793400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:94791800-94794200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:94791800-94794600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:94791800-94796200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:94792000-94792600	Enhancers	H1 Cell Line	embryonic stem cell

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