Variant report

Variant	rs12036256
Chromosome Location	chr1:70818576-70818577
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70818121-70818589	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr1:70818511-70819085	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:70818358-70820986	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70817791..70820390-chr1:70876768..70878594,3	MCF-7	breast:
2	chr1:70799533..70801212-chr1:70816344..70819008,2	K562	blood:
3	chr1:70697900..70700190-chr1:70817863..70820129,2	MCF-7	breast:
4	chr1:70686799..70689606-chr1:70818481..70820974,3	K562	blood:
5	chr1:70693400..70696286-chr1:70816820..70818777,2	K562	blood:
6	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
7	chr1:70814864..70817394-chr1:70817734..70820008,3	MCF-7	breast:
8	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:

No data

Variant related genes	Relation type
HHLA3	TF binding region
ENSG00000116754	Chromatin interaction
ENSG00000116761	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10465863	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10889868	0.86[CHD][hapmap]
rs11209599	1.00[CEU][hapmap]
rs11209600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11209602	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11209603	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11209605	0.82[CHD][hapmap]
rs11209608	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11209611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11800138	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12028257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12029977	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12030275	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs12031053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12034101	0.83[AMR][1000 genomes]
rs12037272	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];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12042565	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565458	0.82[AMR][1000 genomes]
rs1327873	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs17131276	0.83[CEU][hapmap]
rs17131285	0.83[CEU][hapmap]
rs1969953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4650038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4650041	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4650047	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs56211824	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58997663	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59821213	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60602940	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61122312	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61587863	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61678482	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72678630	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72678644	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72678645	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72678646	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768433	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs998523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv871430	chr1:70765659-70819912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12036256	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs12036256	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
3	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:70799600-70818600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:70800400-70819200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:70800400-70819200	Weak transcription	Placenta	Placenta
7	chr1:70805000-70819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:70809400-70819400	Weak transcription	Spleen	Spleen
9	chr1:70810400-70818800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:70811600-70819000	Weak transcription	Stomach Mucosa	stomach
11	chr1:70816000-70819000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:70816400-70818600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:70816600-70819000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:70816800-70819000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:70816800-70819400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:70817000-70821000	Active TSS	Fetal Brain Female	brain
17	chr1:70817400-70818600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:70817400-70819000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:70817600-70818600	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:70817600-70818600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:70817600-70818800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:70817600-70819000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:70817600-70820600	Active TSS	Brain Angular Gyrus	brain
24	chr1:70817600-70821200	Active TSS	NHLF	lung
25	chr1:70817600-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:70817600-70821600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:70817600-70822000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:70817800-70818600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:70817800-70818600	Enhancers	Fetal Stomach	stomach
30	chr1:70817800-70819000	Weak transcription	Small Intestine	intestine
31	chr1:70817800-70819200	Weak transcription	Lung	lung
32	chr1:70817800-70819400	Flanking Active TSS	Dnd41	blood
33	chr1:70817800-70820800	Active TSS	GM12878-XiMat	blood
34	chr1:70817800-70821400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:70818000-70818600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:70818000-70818600	Weak transcription	Fetal Intestine Small	intestine
37	chr1:70818000-70818800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:70818000-70818800	Flanking Active TSS	Fetal Brain Male	brain
39	chr1:70818000-70819000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:70818000-70819000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:70818000-70819000	Weak transcription	Left Ventricle	heart
42	chr1:70818000-70819200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:70818000-70819200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:70818000-70819200	Weak transcription	Pancreas	Pancrea
45	chr1:70818000-70819200	Flanking Active TSS	HUVEC	blood vessel
46	chr1:70818000-70820600	Active TSS	NH-A	brain
47	chr1:70818000-70820800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:70818000-70820800	Active TSS	Fetal Kidney	kidney
49	chr1:70818000-70820800	Active TSS	K562	blood
50	chr1:70818000-70820800	Active TSS	NHDF-Ad	bronchial

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