Variant report

Variant	rs11171856
Chromosome Location	chr12:56841819-56841820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56751886..56753976-chr12:56841675..56844416,2	MCF-7	breast:
2	chr12:56839562..56844740-chr12:56860089..56866019,9	MCF-7	breast:
3	chr12:56841673..56844476-chr12:56882161..56884243,2	MCF-7	breast:
4	chr12:56841526..56846188-chr12:56861608..56864760,4	K562	blood:
5	chr12:56815165..56817428-chr12:56841549..56843141,2	MCF-7	breast:
6	chr12:56510141..56512052-chr12:56841744..56844555,2	MCF-7	breast:
7	chr12:56836758..56838367-chr12:56840273..56842942,2	K562	blood:
8	chr12:56753203..56755632-chr12:56841567..56843289,3	MCF-7	breast:
9	chr12:56707797..56709815-chr12:56841516..56843203,2	MCF-7	breast:
10	chr12:56838620..56841203-chr12:56841279..56843088,2	MCF-7	breast:
11	chr12:56693766..56695727-chr12:56841370..56844312,2	K562	blood:
12	chr12:56827122..56829878-chr12:56841273..56843034,2	K562	blood:
13	chr12:56753916..56755760-chr12:56841528..56845904,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111602	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000139641	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10876889	0.85[ASN][1000 genomes]
rs10876890	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11171847	0.88[ASN][1000 genomes]
rs11171848	0.90[ASN][1000 genomes]
rs11171849	0.90[ASN][1000 genomes]
rs11171850	0.82[CEU][hapmap];0.88[CHB][hapmap];0.90[ASN][1000 genomes]
rs11171852	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11610921	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11833581	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11833583	0.89[ASN][1000 genomes]
rs12299614	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs12313431	0.89[ASN][1000 genomes]
rs12316810	0.94[ASN][1000 genomes]
rs12815993	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976294	0.83[ASN][1000 genomes]
rs2279665	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs2291738	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs2371455	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2638304	0.87[ASN][1000 genomes]
rs2657882	0.84[ASN][1000 genomes]
rs2657883	0.87[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2939303	0.92[ASN][1000 genomes]
rs34520497	0.88[ASN][1000 genomes]
rs34644700	0.90[ASN][1000 genomes]
rs35634983	0.86[ASN][1000 genomes]
rs3782237	0.89[ASN][1000 genomes]
rs3809125	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs6581094	0.89[ASN][1000 genomes]
rs6581095	0.89[ASN][1000 genomes]
rs67027355	0.89[ASN][1000 genomes]
rs703829	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs7312888	0.83[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs774026	0.89[ASN][1000 genomes]
rs774027	0.82[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs774031	0.89[ASN][1000 genomes]
rs774032	0.89[ASN][1000 genomes]
rs774033	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs774034	0.85[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs774035	0.82[CEU][hapmap];0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs774036	0.81[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs774037	0.89[ASN][1000 genomes]
rs774039	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs774047	0.82[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs7977477	0.82[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs812278	0.83[ASN][1000 genomes]
rs812279	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11171856	NACA	cis	cerebellum	SCAN
rs11171856	AMHR2	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56811800-56842400	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:56813000-56842600	Weak transcription	Fetal Heart	heart
3	chr12:56813800-56842400	Weak transcription	Right Atrium	heart
4	chr12:56816200-56842400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:56825400-56842000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:56826200-56842400	Weak transcription	NH-A	brain
7	chr12:56826400-56842200	Weak transcription	HSMM	muscle
8	chr12:56826400-56842400	Weak transcription	NHDF-Ad	bronchial
9	chr12:56827200-56842600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:56827800-56842200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:56827800-56842400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:56827800-56842400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:56827800-56842400	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:56827800-56842400	Weak transcription	Fetal Stomach	stomach
15	chr12:56827800-56842400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:56827800-56842600	Weak transcription	Spleen	Spleen
17	chr12:56828000-56842200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:56828000-56842400	Weak transcription	Fetal Thymus	thymus
19	chr12:56828000-56842400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:56828000-56842400	Weak transcription	Thymus	Thymus
21	chr12:56836600-56842400	Weak transcription	HMEC	breast
22	chr12:56837000-56842600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:56837600-56842400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:56838200-56842400	Weak transcription	NHEK	skin
25	chr12:56838400-56842400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:56838600-56842000	Weak transcription	Fetal Intestine Large	intestine
27	chr12:56838600-56842400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:56838600-56842600	Weak transcription	Left Ventricle	heart
29	chr12:56838800-56842200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:56838800-56842200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:56838800-56842200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:56838800-56842400	Weak transcription	Fetal Intestine Small	intestine
33	chr12:56838800-56842400	Weak transcription	Placenta	Placenta
34	chr12:56839000-56842400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:56839800-56842200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:56841200-56842000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr12:56841200-56842000	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:56841200-56842200	Enhancers	HepG2	liver
39	chr12:56841200-56842400	Enhancers	HUVEC	blood vessel
40	chr12:56841400-56842200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:56841400-56842200	Enhancers	Liver	Liver
42	chr12:56841400-56842200	Weak transcription	Fetal Kidney	kidney
43	chr12:56841400-56842400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:56841400-56842400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:56841400-56842400	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:56841400-56842400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:56841600-56842200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:56841600-56842200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:56841600-56842400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:56841600-56843400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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