Variant report

Variant	rs12952
Chromosome Location	chr6:486193-486194
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	chr6:479740..482609-chr6:484854..487797,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10900954	0.99[EUR][1000 genomes]
rs11242914	0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4072107	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392037	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs950039	0.94[ASN][1000 genomes]
rs974455	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428134	chr6:60001-653718	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2758034	chr6:60001-775274	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2759401	chr6:60001-775274	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv531999	chr6:163083-588213	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1067791	chr6:163083-919234	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv497978	chr6:163083-919234	ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv432823	chr6:165391-516350	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv1024273	chr6:170425-510748	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv538028	chr6:170425-510748	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1032462	chr6:170425-766201	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv538029	chr6:170425-766201	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1034089	chr6:183203-714494	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv538053	chr6:230804-757589	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv1016410	chr6:259527-499709	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv538055	chr6:259527-499709	Weak transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
16	nsv533283	chr6:265806-588274	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	nsv1032977	chr6:266046-538203	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
18	nsv538064	chr6:266046-538203	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
19	nsv432841	chr6:367109-722716	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv883359	chr6:394293-516350	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
21	nsv830569	chr6:402743-573991	Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
22	nsv600781	chr6:403799-833579	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
23	nsv5167	chr6:442174-486632	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv948643	chr6:455419-1113509	Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
25	nsv948744	chr6:472807-1178561	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
26	nsv1023195	chr6:474826-737503	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv538070	chr6:474826-737503	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv1015678	chr6:474826-866394	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv538071	chr6:474826-866394	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12952	GMDS	cis	parietal	SCAN
rs12952	FOXF2	cis	cerebellum	SCAN
rs12952	FAM50B	cis	parietal	SCAN
rs12952	EXOC2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:475600-487600	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:475600-487800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:475600-489000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:475600-498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:475600-511000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:475600-515200	Weak transcription	Brain Germinal Matrix	brain
7	chr6:475800-488600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:475800-489200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:479200-488600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:479400-486200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:479400-488000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:479400-495600	Weak transcription	HepG2	liver
13	chr6:480800-502400	Weak transcription	Fetal Heart	heart
14	chr6:481000-505400	Weak transcription	Fetal Brain Male	brain
15	chr6:481000-513000	Weak transcription	Psoas Muscle	Psoas
16	chr6:481200-488600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:481400-487200	Weak transcription	Brain Substantia Nigra	brain
18	chr6:482400-488000	Weak transcription	Fetal Intestine Large	intestine
19	chr6:482400-488200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:483000-492200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:483000-520800	Weak transcription	HSMM	muscle
22	chr6:483200-495600	Weak transcription	NHDF-Ad	bronchial
23	chr6:483400-506600	Weak transcription	A549	lung
24	chr6:483600-495800	Weak transcription	Small Intestine	intestine
25	chr6:483800-488000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:484000-486800	Weak transcription	Osteobl	bone
27	chr6:484000-487600	Weak transcription	Stomach Mucosa	stomach
28	chr6:484000-502000	Weak transcription	Colonic Mucosa	Colon
29	chr6:484200-486200	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr6:484200-487600	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:484200-489000	Strong transcription	Fetal Lung	lung
32	chr6:484400-486200	Strong transcription	Primary B cells from cord blood	blood
33	chr6:484400-486400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
34	chr6:484400-486800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:484400-487000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:484400-487400	Strong transcription	Primary T cells from cord blood	blood
37	chr6:484400-488200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:484400-488400	ZNF genes & repeats	Aorta	Aorta
39	chr6:484400-488400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr6:484400-488600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:484400-489000	Strong transcription	Adipose Nuclei	Adipose
42	chr6:484400-490400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:484400-509800	Weak transcription	HUVEC	blood vessel
44	chr6:484600-486400	ZNF genes & repeats	Ovary	ovary
45	chr6:484600-486800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:484600-486800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:484600-486800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:484600-486800	Strong transcription	Gastric	stomach
49	chr6:484600-486800	Strong transcription	HSMMtube	muscle
50	chr6:484600-487000	Strong transcription	Duodenum Mucosa	Duodenum

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