Variant report

Variant	rs11752747
Chromosome Location	chr6:5272671-5272672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5271290..5273704-chr6:5277063..5280709,3	K562	blood:
2	chr6:5271290..5273704-chr6:5277063..5279259,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1570085	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1609808	0.89[EUR][1000 genomes]
rs17140068	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs1807139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2145372	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2224392	0.89[EUR][1000 genomes]
rs2224393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2753222	0.87[EUR][1000 genomes]
rs2753223	0.89[EUR][1000 genomes]
rs2753224	0.89[EUR][1000 genomes]
rs2753228	0.89[EUR][1000 genomes]
rs2753229	0.89[EUR][1000 genomes]
rs2753230	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2753233	0.87[EUR][1000 genomes]
rs2753234	0.87[EUR][1000 genomes]
rs2753235	1.00[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2753236	0.84[EUR][1000 genomes]
rs2753237	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2753238	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2753239	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2753240	0.89[EUR][1000 genomes]
rs2753244	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2753245	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2773298	0.87[EUR][1000 genomes]
rs2773299	0.87[EUR][1000 genomes]
rs2773300	0.84[EUR][1000 genomes]
rs2773304	0.89[EUR][1000 genomes]
rs2773306	0.85[EUR][1000 genomes]
rs2773307	0.88[EUR][1000 genomes]
rs2773308	0.89[EUR][1000 genomes]
rs2773309	0.87[EUR][1000 genomes]
rs2773310	0.89[EUR][1000 genomes]
rs2773311	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2773312	0.88[EUR][1000 genomes]
rs2773314	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2773316	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2773317	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2773318	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2773319	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6597122	0.91[ASN][1000 genomes]
rs6909619	0.87[EUR][1000 genomes]
rs6913120	0.91[EUR][1000 genomes]
rs6926122	1.00[JPT][hapmap]
rs72813693	0.87[EUR][1000 genomes]
rs72813697	0.87[EUR][1000 genomes]
rs72813700	0.86[EUR][1000 genomes]
rs72815603	0.87[EUR][1000 genomes]
rs766339	0.86[EUR][1000 genomes]
rs766340	0.89[EUR][1000 genomes]
rs7751332	1.00[JPT][hapmap]
rs7761816	1.00[CHB][hapmap]
rs7765867	1.00[JPT][hapmap]
rs7769327	1.00[JPT][hapmap]
rs7771926	1.00[JPT][hapmap]
rs797130	1.00[JPT][hapmap]
rs797135	1.00[JPT][hapmap]
rs797136	1.00[JPT][hapmap]
rs797145	1.00[JPT][hapmap]
rs808813	1.00[JPT][hapmap]
rs928170	0.89[EUR][1000 genomes]
rs9328291	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9392666	0.89[EUR][1000 genomes]
rs9405811	0.89[EUR][1000 genomes]
rs9502284	0.91[ASN][1000 genomes]
rs9502286	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9502289	1.00[JPT][hapmap]
rs9504364	0.89[EUR][1000 genomes]
rs9504365	0.89[EUR][1000 genomes]
rs9504375	1.00[JPT][hapmap]
rs9504376	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11752747	FARS2	cis	lymphoblastoid	seeQTL
rs11752747	LYRM4	cis	parietal	SCAN
rs11752747	LYRM4	cis	lymphoblastoid	seeQTL
rs11752747	MGC39372	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5262400-5287200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:5262400-5302400	Weak transcription	Aorta	Aorta
3	chr6:5262600-5275200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:5262600-5287200	Weak transcription	Esophagus	oesophagus
5	chr6:5262600-5287600	Weak transcription	Ovary	ovary
6	chr6:5262800-5273600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:5262800-5274400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:5262800-5277000	Weak transcription	Pancreas	Pancrea
9	chr6:5262800-5279000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:5262800-5287200	Weak transcription	Spleen	Spleen
11	chr6:5262800-5287400	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:5263000-5273400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:5263000-5274400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:5263000-5277200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:5263000-5279000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:5263000-5285200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:5263000-5287200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:5263000-5287400	Weak transcription	Fetal Stomach	stomach
19	chr6:5263000-5287800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:5263000-5301000	Weak transcription	Fetal Brain Male	brain
21	chr6:5263200-5273800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:5263200-5274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:5263200-5278400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:5263200-5278400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:5263200-5279000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:5263200-5280200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:5263200-5287800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:5263400-5276800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:5263400-5281200	Weak transcription	Brain Angular Gyrus	brain
30	chr6:5263400-5287400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:5263400-5287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:5263800-5273000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:5263800-5279000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:5263800-5291800	Weak transcription	Fetal Intestine Small	intestine
35	chr6:5264000-5274400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:5264600-5274200	Weak transcription	Dnd41	blood
37	chr6:5266800-5274400	Weak transcription	Primary T cells from cord blood	blood
38	chr6:5267000-5273800	Weak transcription	GM12878-XiMat	blood
39	chr6:5267000-5290400	Weak transcription	HepG2	liver
40	chr6:5267200-5280200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:5268000-5294400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:5269200-5278400	Weak transcription	Hela-S3	cervix
43	chr6:5270600-5273600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:5271200-5274800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:5271400-5273000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:5271400-5276800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:5271400-5278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:5271400-5280200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:5271600-5273400	Enhancers	NHEK	skin
50	chr6:5271600-5276600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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