Variant report

Variant	rs4712859
Chromosome Location	chr6:24826572-24826573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10806995	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11965640	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12524169	0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12662984	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12662998	0.86[EUR][1000 genomes]
rs35374726	0.82[AFR][1000 genomes]
rs4397217	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4507579	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4610554	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712851	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712853	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712855	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712858	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55640933	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56733961	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56890646	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60135217	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60182091	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60390507	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60776362	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61528548	0.87[EUR][1000 genomes]
rs62401976	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62401977	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6927418	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7756233	0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7773439	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348646	0.86[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9348648	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9348649	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9358800	0.91[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9358802	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366582	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9366583	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379695	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4712859	RP11-367G6.1	cis	multi-tissue	Pritchard
rs4712859	ZNF391	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
3	chr6:24788000-24832000	Weak transcription	Brain Substantia Nigra	brain
4	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:24789200-24842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:24798200-24827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:24798200-24841200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:24800000-24843200	Weak transcription	Liver	Liver
9	chr6:24802600-24834200	Weak transcription	HSMM	muscle
10	chr6:24802800-24827400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:24803400-24827400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:24804800-24858200	Weak transcription	Gastric	stomach
13	chr6:24806200-24842400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:24808800-24845600	Weak transcription	Fetal Stomach	stomach
15	chr6:24809800-24827400	Weak transcription	GM12878-XiMat	blood
16	chr6:24809800-24839200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:24810000-24827400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:24810000-24831600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:24810000-24832600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:24810200-24827400	Weak transcription	Brain Germinal Matrix	brain
21	chr6:24810600-24827400	Weak transcription	Left Ventricle	heart
22	chr6:24810600-24827400	Weak transcription	Lung	lung
23	chr6:24817800-24827600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr6:24817800-24829600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:24817800-24836000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:24817800-24839600	Strong transcription	Primary T cells from cord blood	blood
27	chr6:24817800-24840800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:24817800-24854400	Strong transcription	Primary B cells from cord blood	blood
29	chr6:24817800-24855800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:24818000-24827200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:24818000-24827800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:24818000-24836200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:24818000-24840000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:24818000-24840600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:24818000-24840600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:24818600-24855800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:24818800-24856000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:24818800-24856400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:24819000-24827200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:24821400-24834400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:24821400-24836000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr6:24821600-24828200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:24821800-24827800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:24821800-24828400	Strong transcription	Fetal Thymus	thymus
45	chr6:24822200-24827400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:24822400-24826800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:24822400-24827200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:24822400-24827400	Weak transcription	Pancreas	Pancrea
49	chr6:24822400-24840200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:24822600-24844000	Weak transcription	Fetal Heart	heart

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