Variant report

Variant	rs1250880
Chromosome Location	chr1:76196602-76196603
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	GATA2	chr1:76196395-76196604	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr1:76196377-76196745	K562	blood:	n/a	n/a
3	POLR2A	chr1:76195766-76196651	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
2	chr1:76190052..76193339-chr1:76196508..76198872,3	K562	blood:
3	chr1:76177430..76180048-chr1:76194109..76196652,2	K562	blood:

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

Extended variants
information (count: 140 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1001160	0.81[CEU][hapmap]
rs1021462	0.86[CHB][hapmap]
rs10873738	0.85[JPT][hapmap]
rs10873797	0.81[CEU][hapmap]
rs1093006	0.83[ASN][1000 genomes]
rs1093009	0.83[ASN][1000 genomes]
rs11161439	0.84[ASN][1000 genomes]
rs11161447	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11161465	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11161600	0.80[ASN][1000 genomes]
rs11161602	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs11161731	0.82[CHB][hapmap]
rs11161848	0.81[CEU][hapmap]
rs11161852	0.82[CHB][hapmap]
rs11161887	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs11164035	0.84[ASN][1000 genomes]
rs11164037	0.84[ASN][1000 genomes]
rs1144333	0.80[CHB][hapmap]
rs1146572	0.89[ASN][1000 genomes]
rs1146577	0.83[ASN][1000 genomes]
rs1146587	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146592	0.85[ASN][1000 genomes]
rs1146593	0.83[ASN][1000 genomes]
rs1146648	0.81[JPT][hapmap]
rs1146651	0.81[JPT][hapmap]
rs11578480	0.88[CEU][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap]
rs11588643	0.81[CEU][hapmap]
rs1159215	0.81[CEU][hapmap]
rs12021750	0.82[CHB][hapmap]
rs12022011	0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12024645	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12027620	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs12032051	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12033058	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12044025	0.86[JPT][hapmap]
rs12045299	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12076093	0.81[JPT][hapmap]
rs12090712	0.81[JPT][hapmap]
rs12130832	0.87[CEU][hapmap]
rs12131344	0.92[CEU][hapmap]
rs12132750	0.91[CEU][hapmap]
rs12138018	0.88[AFR][1000 genomes]
rs12142247	0.87[CEU][hapmap]
rs12401729	0.81[CHB][hapmap]
rs12407107	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12409592	0.82[CHB][hapmap]
rs1250875	0.89[ASN][1000 genomes]
rs1250876	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]
rs1250877	0.89[ASN][1000 genomes]
rs1250878	0.89[ASN][1000 genomes]
rs1251065	0.89[ASN][1000 genomes]
rs1251078	0.86[JPT][hapmap]
rs1251079	0.86[JPT][hapmap]
rs12563737	0.90[ASN][1000 genomes]
rs12728962	0.80[ASN][1000 genomes]
rs12732722	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12744608	0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12745456	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12747967	0.84[ASN][1000 genomes]
rs12756349	0.80[ASN][1000 genomes]
rs1303870	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1323734	0.83[ASN][1000 genomes]
rs1391518	0.84[ASN][1000 genomes]
rs1391520	0.84[ASN][1000 genomes]
rs1498311	0.81[CEU][hapmap]
rs1498313	0.81[JPT][hapmap]
rs1603734	0.81[JPT][hapmap]
rs1621198	0.83[ASN][1000 genomes]
rs1628063	0.81[CEU][hapmap]
rs1631498	0.83[ASN][1000 genomes]
rs1689270	0.80[CEU][hapmap]
rs1694421	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1694428	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs17097681	0.81[CHB][hapmap]
rs17647178	0.88[CEU][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap]
rs1767457	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1767459	0.85[ASN][1000 genomes]
rs1770513	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17848068	0.87[AFR][1000 genomes]
rs1796827	0.81[CEU][hapmap]
rs1826978	0.85[ASN][1000 genomes]
rs1846233	0.92[CEU][hapmap]
rs1908089	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1960528	0.83[ASN][1000 genomes]
rs2029682	0.81[CEU][hapmap]
rs35290302	0.82[CHB][hapmap]
rs35837767	0.84[ASN][1000 genomes]
rs3737574	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3765682	0.81[CHB][hapmap]
rs3819949	0.82[CHB][hapmap]
rs4638068	0.92[CEU][hapmap]
rs5745314	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5745331	0.81[CEU][hapmap]
rs5745334	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5745347	0.81[CEU][hapmap]
rs5745429	0.82[CHB][hapmap]
rs5745430	0.80[CEU][hapmap]
rs5745448	0.80[JPT][hapmap]
rs5745465	0.81[CHB][hapmap]
rs5745523	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5745532	0.85[CHB][hapmap]
rs5745542	0.81[CHB][hapmap]
rs5745543	0.83[CEU][hapmap]
rs5745545	0.80[CEU][hapmap]
rs5745546	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs5745547	0.80[CEU][hapmap]
rs60550898	0.89[AFR][1000 genomes]
rs6656501	0.81[CEU][hapmap]
rs6676182	0.90[ASN][1000 genomes]
rs6687882	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[TSI][hapmap]
rs6695055	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6704444	0.93[AFR][1000 genomes]
rs67108483	0.84[ASN][1000 genomes]
rs696677	0.82[ASN][1000 genomes]
rs696679	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs699677	0.83[ASN][1000 genomes]
rs699683	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs699824	0.83[ASN][1000 genomes]
rs699825	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs71502708	0.83[ASN][1000 genomes]
rs74090722	0.93[AFR][1000 genomes]
rs74090730	0.93[AFR][1000 genomes]
rs7514912	0.81[JPT][hapmap]
rs7516477	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525919	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7548391	0.81[JPT][hapmap]
rs7548695	0.89[ASN][1000 genomes]
rs7548991	0.86[CHB][hapmap];0.95[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];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs815301	0.83[ASN][1000 genomes]
rs815303	0.81[ASN][1000 genomes]
rs815305	0.82[ASN][1000 genomes]
rs815309	0.86[ASN][1000 genomes]
rs9660848	0.86[CHB][hapmap];0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1250880	SNORD45B	cis	parietal	SCAN
rs1250880	SNORD45B	cis	cerebellum	SCAN
rs1250880	CRYZ	cis	lymphoblastoid	seeQTL
rs1250880	PIGK	cis	parietal	SCAN
rs1250880	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76190800-76199400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:76190800-76207200	Weak transcription	Spleen	Spleen
3	chr1:76190800-76208000	Weak transcription	Gastric	stomach
4	chr1:76191000-76199000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:76191200-76197600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:76191400-76199200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:76191400-76199400	Weak transcription	Aorta	Aorta
9	chr1:76191800-76208000	Weak transcription	A549	lung
10	chr1:76191800-76208200	Weak transcription	Brain Substantia Nigra	brain
11	chr1:76191800-76209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:76192000-76197400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:76192000-76198600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:76192000-76198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:76192000-76198600	Weak transcription	HSMMtube	muscle
16	chr1:76192000-76199400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:76192000-76199400	Weak transcription	Lung	lung
18	chr1:76192000-76208000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:76192000-76210200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:76192200-76198200	Weak transcription	Fetal Intestine Large	intestine
24	chr1:76192200-76198400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:76192200-76198800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:76192200-76199200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:76192200-76200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:76192200-76200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:76192200-76200400	Weak transcription	Placenta	Placenta
30	chr1:76192200-76204600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
32	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:76192400-76197200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:76192400-76197400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:76192400-76197400	Weak transcription	Primary T cells from cord blood	blood
36	chr1:76192400-76197400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:76192400-76197400	Weak transcription	NHDF-Ad	bronchial
38	chr1:76192400-76197600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:76192400-76197800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:76192400-76197800	Weak transcription	Osteobl	bone
41	chr1:76192400-76198000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:76192400-76198200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:76192400-76198200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:76192400-76198400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:76192400-76198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:76192400-76198600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:76192400-76198600	Weak transcription	Fetal Lung	lung
48	chr1:76192400-76198600	Weak transcription	HSMM	muscle
49	chr1:76192400-76198600	Weak transcription	NH-A	brain
50	chr1:76192400-76199200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links