Variant report

Variant	rs1250876
Chromosome Location	chr1:76193232-76193233
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	ARID3A	chr1:76193195-76193385	K562	blood:	n/a	n/a
2	MAZ	chr1:76193057-76193773	GM12878	blood:	n/a	n/a
3	EP300	chr1:76192780-76193438	GM12878	blood:	n/a	n/a
4	IRF1	chr1:76189245-76193364	K562	blood:	n/a	chr1:76189864-76189877 chr1:76190686-76190700 chr1:76190686-76190696 chr1:76192789-76192803 chr1:76190682-76190696 chr1:76192789-76192800 chr1:76190680-76190697 chr1:76190381-76190395 chr1:76189864-76189878 chr1:76189864-76189876 chr1:76190001-76190015 chr1:76190685-76190696 chr1:76192789-76192802 chr1:76190176-76190187 chr1:76193209-76193221 chr1:76192989-76193000 chr1:76192790-76192800 chr1:76189863-76189874 chr1:76189864-76189877 chr1:76191327-76191339 chr1:76192789-76192802 chr1:76192790-76192804 chr1:76192989-76193003 chr1:76190684-76190704 chr1:76192789-76192802 chr1:76189859-76189876
5	TBL1XR1	chr1:76192660-76193256	GM12878	blood:	n/a	n/a
6	RCOR1	chr1:76193197-76193497	GM12878	blood:	n/a	n/a
7	ATF2	chr1:76192624-76193289	GM12878	blood:	n/a	n/a
8	CEBPB	chr1:76192971-76193526	K562	blood:	n/a	chr1:76193126-76193137 chr1:76193128-76193137
9	BHLHE40	chr1:76192365-76193431	GM12878	blood:	n/a	n/a
10	EP300	chr1:76192612-76193324	GM12878	blood:	n/a	n/a
11	RUNX3	chr1:76192238-76193659	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:75934636..75936669-chr1:76193127..76195034,2	K562	blood:
2	chr1:76135232..76136937-chr1:76193196..76195615,2	K562	blood:
3	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
4	chr1:76190052..76193339-chr1:76196508..76198872,3	K562	blood:
5	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:
6	chr1:76192256..76194565-chr1:76250720..76252773,2	MCF-7	breast:
7	chr1:76189028..76194220-chr1:76209012..76215464,6	K562	blood:
8	chr1:76189426..76191146-chr1:76192491..76194847,2	MCF-7	breast:
9	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:

Variant related genes	Relation type
ACADM	TF binding region
ENSG00000178193	TF binding region
ENSG00000057468	Chromatin interaction
ENSG00000207241	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000201487	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs1001160	0.84[CEU][hapmap]
rs1021462	0.86[CHB][hapmap]
rs10873738	0.90[JPT][hapmap]
rs10873797	0.84[CEU][hapmap]
rs1093006	0.83[ASN][1000 genomes]
rs1093009	0.83[ASN][1000 genomes]
rs11161439	0.85[ASN][1000 genomes]
rs11161447	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11161465	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11161600	0.81[ASN][1000 genomes]
rs11161602	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11161731	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11161848	0.84[CEU][hapmap]
rs11161852	0.82[CHB][hapmap]
rs11161887	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs11164035	0.85[ASN][1000 genomes]
rs11164037	0.85[ASN][1000 genomes]
rs1144328	0.81[JPT][hapmap]
rs1144331	0.81[JPT][hapmap]
rs1144333	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1144337	0.81[JPT][hapmap]
rs1144342	0.81[JPT][hapmap]
rs1146572	0.88[ASN][1000 genomes]
rs1146577	0.82[ASN][1000 genomes]
rs1146587	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146592	0.84[ASN][1000 genomes]
rs1146593	0.83[ASN][1000 genomes]
rs1146647	0.81[JPT][hapmap]
rs1146648	0.86[JPT][hapmap]
rs1146649	0.81[JPT][hapmap]
rs1146651	0.85[JPT][hapmap]
rs1146652	0.81[JPT][hapmap]
rs11578480	0.92[CEU][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap]
rs11588643	0.84[CEU][hapmap]
rs1159215	0.84[CEU][hapmap]
rs12021750	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12022011	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12024645	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12027620	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12032051	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12033058	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12044025	0.90[JPT][hapmap]
rs12045299	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12076093	0.86[JPT][hapmap]
rs12090712	0.85[JPT][hapmap]
rs12130832	0.91[CEU][hapmap]
rs12131344	0.96[CEU][hapmap]
rs12132750	0.95[CEU][hapmap]
rs12138018	0.92[AFR][1000 genomes]
rs12142247	0.91[CEU][hapmap]
rs12401729	0.81[CHB][hapmap]
rs12407107	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12409592	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1250875	0.88[ASN][1000 genomes]
rs1250877	0.88[ASN][1000 genomes]
rs1250878	0.88[ASN][1000 genomes]
rs1250880	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1251065	0.88[ASN][1000 genomes]
rs1251078	0.91[JPT][hapmap]
rs1251079	0.91[JPT][hapmap]
rs1251272	0.84[JPT][hapmap]
rs1251274	0.81[JPT][hapmap]
rs12563737	0.90[ASN][1000 genomes]
rs12703	0.81[JPT][hapmap]
rs12728962	0.81[ASN][1000 genomes]
rs12732722	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12744608	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12745456	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12747967	0.85[ASN][1000 genomes]
rs12756349	0.81[ASN][1000 genomes]
rs12757213	0.80[ASN][1000 genomes]
rs1303870	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs1323734	0.83[ASN][1000 genomes]
rs1391518	0.85[ASN][1000 genomes]
rs1391520	0.85[ASN][1000 genomes]
rs1498311	0.84[CEU][hapmap]
rs1498313	0.86[JPT][hapmap]
rs1603734	0.86[JPT][hapmap]
rs1621198	0.83[ASN][1000 genomes]
rs1628063	0.84[CEU][hapmap]
rs1631498	0.83[ASN][1000 genomes]
rs1689270	0.84[CEU][hapmap]
rs1694421	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1694428	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17097681	0.81[CHB][hapmap]
rs17647178	0.92[CEU][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap]
rs1767457	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1767459	0.84[ASN][1000 genomes]
rs1770513	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17848068	0.91[AFR][1000 genomes]
rs1796827	0.84[CEU][hapmap]
rs1826978	0.85[ASN][1000 genomes]
rs1846233	0.96[CEU][hapmap]
rs1856791	0.83[CEU][hapmap]
rs1908089	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1960528	0.83[ASN][1000 genomes]
rs2029682	0.84[CEU][hapmap]
rs2307077	0.81[JPT][hapmap]
rs35290302	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs35837767	0.85[ASN][1000 genomes]
rs3737574	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3765682	0.81[CHB][hapmap]
rs3819949	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4638068	0.96[CEU][hapmap]
rs5745314	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs5745327	0.81[JPT][hapmap]
rs5745331	0.84[CEU][hapmap]
rs5745334	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs5745343	0.81[JPT][hapmap]
rs5745347	0.84[CEU][hapmap]
rs5745383	0.83[CEU][hapmap]
rs5745392	0.81[JPT][hapmap]
rs5745394	0.83[CEU][hapmap]
rs5745429	0.82[CHB][hapmap]
rs5745430	0.84[CEU][hapmap]
rs5745448	0.80[JPT][hapmap]
rs5745451	0.81[JPT][hapmap]
rs5745465	0.81[CHB][hapmap]
rs5745523	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs5745532	0.85[CHB][hapmap]
rs5745542	0.81[CHB][hapmap]
rs5745543	0.83[CEU][hapmap]
rs5745545	0.84[CEU][hapmap]
rs5745546	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5745547	0.84[CEU][hapmap]
rs60550898	0.85[AFR][1000 genomes]
rs6656501	0.84[CEU][hapmap]
rs6676182	0.90[ASN][1000 genomes]
rs6687882	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs6695055	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6704444	0.89[AFR][1000 genomes]
rs67108483	0.85[ASN][1000 genomes]
rs696677	0.81[ASN][1000 genomes]
rs696679	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs699677	0.83[ASN][1000 genomes]
rs699683	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs699824	0.83[ASN][1000 genomes]
rs699825	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs71502708	0.84[ASN][1000 genomes]
rs74090722	0.89[AFR][1000 genomes]
rs74090730	0.89[AFR][1000 genomes]
rs7514912	0.86[JPT][hapmap]
rs7516477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525919	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7548391	0.86[JPT][hapmap]
rs7548695	0.90[ASN][1000 genomes]
rs7548991	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs814851	0.83[ASN][1000 genomes]
rs814855	0.83[ASN][1000 genomes]
rs814897	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs815301	0.83[ASN][1000 genomes]
rs815303	0.80[ASN][1000 genomes]
rs815305	0.83[ASN][1000 genomes]
rs815309	0.86[ASN][1000 genomes]
rs9660848	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1250876	PIGK	cis	parietal	SCAN
rs1250876	SNORD45B	cis	cerebellum	SCAN
rs1250876	SNORD45B	cis	parietal	SCAN
rs1250876	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76189800-76193400	Active TSS	K562	blood
2	chr1:76189800-76194200	Active TSS	GM12878-XiMat	blood
3	chr1:76190800-76199400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:76190800-76207200	Weak transcription	Spleen	Spleen
5	chr1:76190800-76208000	Weak transcription	Gastric	stomach
6	chr1:76191000-76199000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:76191200-76193800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:76191200-76197600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:76191400-76194000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:76191400-76199200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:76191400-76199400	Weak transcription	Aorta	Aorta
13	chr1:76191600-76193400	Enhancers	Primary B cells from cord blood	blood
14	chr1:76191800-76193400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:76191800-76195800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:76191800-76208000	Weak transcription	A549	lung
17	chr1:76191800-76208200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:76191800-76209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:76192000-76193400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:76192000-76193400	Weak transcription	Pancreas	Pancrea
21	chr1:76192000-76193400	Weak transcription	Right Ventricle	heart
22	chr1:76192000-76193600	Weak transcription	Esophagus	oesophagus
23	chr1:76192000-76193800	Enhancers	Fetal Brain Female	brain
24	chr1:76192000-76193800	Enhancers	Psoas Muscle	Psoas
25	chr1:76192000-76195200	Weak transcription	Fetal Stomach	stomach
26	chr1:76192000-76195800	Weak transcription	Left Ventricle	heart
27	chr1:76192000-76196200	Weak transcription	Fetal Thymus	thymus
28	chr1:76192000-76196400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:76192000-76197400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:76192000-76198600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:76192000-76198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:76192000-76198600	Weak transcription	HSMMtube	muscle
33	chr1:76192000-76199400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:76192000-76199400	Weak transcription	Lung	lung
35	chr1:76192000-76208000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:76192000-76210200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:76192200-76193800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:76192200-76198200	Weak transcription	Fetal Intestine Large	intestine
42	chr1:76192200-76198400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:76192200-76198800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:76192200-76199200	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:76192200-76200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:76192200-76200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:76192200-76200400	Weak transcription	Placenta	Placenta
48	chr1:76192200-76204600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
50	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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