Variant report

Variant	rs11714957
Chromosome Location	chr3:49776178-49776179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49774827..49777820-chr3:49822579..49825134,2	K562	blood:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049413	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1049256	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10865958	0.89[ASN][1000 genomes]
rs10865959	0.88[CHB][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130216	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130218	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130219	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130221	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1128535	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11709680	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11710675	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715304	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11716575	0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11717256	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717463	0.96[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];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920900	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12381242	0.94[ASN][1000 genomes]
rs12490656	0.92[ASN][1000 genomes]
rs12496226	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063621	0.96[ASN][1000 genomes]
rs13084243	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085679	0.89[ASN][1000 genomes]
rs13086130	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090611	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317140	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316065	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491986	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1799843	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799845	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234385	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234391	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2246832	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2247036	0.87[ASN][1000 genomes]
rs2271960	0.96[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2271961	0.96[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2276864	0.96[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291542	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307021	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352967	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352974	0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2352975	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34451146	0.96[ASN][1000 genomes]
rs34522271	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614773	0.94[ASN][1000 genomes]
rs34735338	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35210174	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35261599	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35474403	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749237	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3749241	0.96[ASN][1000 genomes]
rs3811695	0.92[ASN][1000 genomes]
rs3811696	0.94[ASN][1000 genomes]
rs3819325	0.84[ASN][1000 genomes]
rs4519692	0.83[ASN][1000 genomes]
rs4768	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855841	0.91[ASN][1000 genomes]
rs4855850	0.92[ASN][1000 genomes]
rs4855862	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855867	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs57648519	0.96[ASN][1000 genomes]
rs59906301	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60205400	0.96[ASN][1000 genomes]
rs62260715	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260719	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260729	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446295	0.99[ASN][1000 genomes]
rs6766836	0.96[ASN][1000 genomes]
rs6775384	0.92[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6785549	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6802890	0.91[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6804655	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs695238	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs71324996	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7372725	0.88[ASN][1000 genomes]
rs7372730	0.90[ASN][1000 genomes]
rs7372966	0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[ASN][1000 genomes]
rs7374183	0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[ASN][1000 genomes]
rs7374277	0.88[ASN][1000 genomes]
rs7429353	0.88[ASN][1000 genomes]
rs7431078	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431106	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.96[ASN][1000 genomes]
rs7618501	0.98[ASN][1000 genomes]
rs7618519	0.99[ASN][1000 genomes]
rs7629936	0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs7634886	0.94[ASN][1000 genomes]
rs7634902	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7645061	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7648987	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7649348	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9814765	0.94[ASN][1000 genomes]
rs9815766	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9819511	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850465	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9853458	0.94[ASN][1000 genomes]
rs9855505	0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[ASN][1000 genomes]
rs9859153	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9865480	0.94[ASN][1000 genomes]
rs9871654	0.95[ASN][1000 genomes]
rs9872864	0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[ASN][1000 genomes]
rs9873183	0.89[ASN][1000 genomes]
rs9876508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9882639	0.96[ASN][1000 genomes]

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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv967216	chr3:49764885-49776535	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11714957	AMT	cis	cerebellum	SCAN
rs11714957	RBM6	cis	parietal	SCAN
rs11714957	P4HTM	cis	parietal	SCAN
rs11714957	WDR6	cis	parietal	SCAN
rs11714957	RNF123	cis	cerebellum	SCAN
rs11714957	ALS2CL	cis	cerebellum	SCAN
rs11714957	RBM6	cis	Nerve Tibial	GTEx
rs11714957	WDR6	cis	Whole Blood	GTEx
rs11714957	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11714957	CCDC71	cis	cerebellum	SCAN
rs11714957	UCN2	cis	cerebellum	SCAN
rs11714957	C3orf54	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762000-49778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49762400-49776800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:49762400-49781600	Strong transcription	Fetal Stomach	stomach
4	chr3:49762600-49776400	Strong transcription	Fetal Brain Female	brain
5	chr3:49762600-49776800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:49762600-49777000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:49762600-49777200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:49762600-49777600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:49762600-49781800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:49762600-49785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:49762800-49776400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:49762800-49776600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:49763000-49776400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:49763000-49776600	Strong transcription	Placenta	Placenta
16	chr3:49763000-49776800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:49763000-49784800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:49763200-49776400	Strong transcription	Dnd41	blood
19	chr3:49764000-49776400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr3:49764000-49781800	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:49764200-49776600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:49764200-49776600	Strong transcription	Primary T cells from cord blood	blood
23	chr3:49764800-49776600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:49765800-49785800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:49767400-49776400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:49767400-49776400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:49767400-49776400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:49767400-49776400	Strong transcription	Adipose Nuclei	Adipose
29	chr3:49767400-49777600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:49767600-49776400	Strong transcription	Ovary	ovary
31	chr3:49767600-49776400	Strong transcription	Osteobl	bone
32	chr3:49767600-49776600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:49767600-49776600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:49767600-49776800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:49767600-49781400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:49767600-49787800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:49767800-49776200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:49767800-49776200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:49767800-49776200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:49767800-49776400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:49767800-49776400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr3:49767800-49776600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:49768000-49776400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:49768200-49776400	Strong transcription	Fetal Lung	lung
45	chr3:49768200-49787600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:49768400-49776200	Strong transcription	Primary B cells from cord blood	blood
47	chr3:49768400-49776400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr3:49768400-49776400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:49768400-49776600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:49768400-49776600	Strong transcription	NHLF	lung

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