Variant report

Variant	rs11624104
Chromosome Location	chr14:66196137-66196138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10483785	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1054218	0.82[CEU][hapmap]
rs1075566	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158601	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[EUR][1000 genomes]
rs11158611	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621680	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs11622014	0.81[EUR][1000 genomes]
rs11622271	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11622829	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11624045	0.85[EUR][1000 genomes]
rs11625362	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11625882	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11627067	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11627184	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11627185	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11627578	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11627605	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11628765	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11628840	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12050182	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12050231	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12586842	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12588838	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879805	0.83[EUR][1000 genomes]
rs12882200	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12883382	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12886334	0.84[EUR][1000 genomes]
rs12887134	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs12887673	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12887957	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12888212	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12889002	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs12890902	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12894034	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894466	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894902	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12896663	0.85[EUR][1000 genomes]
rs1535173	1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1958561	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs1998036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2064694	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2149841	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs2268961	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2268962	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2300865	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2411351	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2411355	0.83[EUR][1000 genomes]
rs2411357	0.82[EUR][1000 genomes]
rs2411404	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2411405	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3783709	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs4073415	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs4143898	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs4581615	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs4902415	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902416	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6573624	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6573626	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67957534	0.91[EUR][1000 genomes]
rs7142018	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7142165	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7142219	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7142651	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7146742	0.85[CEU][hapmap]
rs7146829	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7149301	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7155541	0.96[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs7157449	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7161123	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs730807	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs743084	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs743085	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7493004	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs761831	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8005710	0.82[EUR][1000 genomes]
rs8010876	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8012278	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs8018278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8022764	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs927004	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9323465	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1045000	chr14:66010886-66372518	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1042671	chr14:66010886-66399888	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11624104	FUT8	cis	cerebellum	SCAN
rs11624104	HIF1A	cis	cerebellum	SCAN
rs11624104	ZFP36L1	cis	parietal	SCAN
rs11624104	VTI1B	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:66179000-66206200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:66184600-66198600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:66185400-66209000	Weak transcription	Brain Angular Gyrus	brain
4	chr14:66186400-66208800	Weak transcription	Fetal Brain Female	brain
5	chr14:66187000-66209000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr14:66187400-66208600	Weak transcription	Placenta	Placenta
7	chr14:66187600-66200000	Weak transcription	Brain Substantia Nigra	brain
8	chr14:66188000-66196800	Strong transcription	Primary B cells from cord blood	blood
9	chr14:66188000-66210800	Weak transcription	Fetal Lung	lung
10	chr14:66188200-66201400	Weak transcription	Psoas Muscle	Psoas
11	chr14:66188400-66197000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:66188400-66210600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr14:66188800-66208800	Weak transcription	Liver	Liver
14	chr14:66189000-66196800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:66189000-66209000	Weak transcription	NHDF-Ad	bronchial
16	chr14:66189600-66210800	Weak transcription	NHLF	lung
17	chr14:66189800-66209000	Weak transcription	HSMMtube	muscle
18	chr14:66190000-66208800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:66190000-66210800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr14:66190200-66197800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr14:66190200-66198400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr14:66190200-66210800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr14:66190400-66198600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr14:66190400-66217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr14:66190600-66196800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:66190600-66197200	Strong transcription	Primary T cells from cord blood	blood
27	chr14:66191600-66212000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr14:66191800-66199800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:66191800-66200000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:66191800-66200800	Weak transcription	Brain Anterior Caudate	brain
31	chr14:66191800-66204400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr14:66191800-66208600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr14:66191800-66208800	Weak transcription	Gastric	stomach
34	chr14:66191800-66208800	Weak transcription	Pancreas	Pancrea
35	chr14:66191800-66210800	Weak transcription	HSMM	muscle
36	chr14:66191800-66217800	Weak transcription	Small Intestine	intestine
37	chr14:66192000-66206800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr14:66192200-66200000	Weak transcription	NH-A	brain
39	chr14:66192200-66208800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr14:66192400-66210200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr14:66192600-66210400	Weak transcription	Right Ventricle	heart
42	chr14:66192800-66196800	Weak transcription	Fetal Brain Male	brain
43	chr14:66192800-66210600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:66192800-66211800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr14:66192800-66212200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr14:66193000-66218800	Weak transcription	Colonic Mucosa	Colon
47	chr14:66193200-66196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr14:66193200-66206600	Strong transcription	Dnd41	blood
49	chr14:66193200-66208800	Weak transcription	Adipose Nuclei	Adipose
50	chr14:66193800-66208800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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