Variant report

Variant	rs9395887
Chromosome Location	chr6:53752877-53752878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1076702	0.81[CHB][hapmap]
rs10948783	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10948784	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12193567	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194768	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12209621	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3935664	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4128619	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4236114	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4260754	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273680	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4331986	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4392712	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4583974	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4612163	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4624872	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645423	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6458967	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6458968	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904545	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6906921	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6907027	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6910777	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6913431	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6935621	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6935838	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7453639	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7745548	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7749635	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7749749	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7755924	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7761285	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7767443	0.82[MKK][hapmap]
rs9296722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296723	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9349682	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9349683	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9349684	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9349685	0.83[ASN][1000 genomes]
rs9349686	0.86[AFR][1000 genomes]
rs9357774	0.82[AFR][1000 genomes]
rs9367543	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9370234	0.82[AMR][1000 genomes]
rs9370237	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370238	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9370240	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382240	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382242	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382243	0.82[CHB][hapmap]
rs9382245	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382247	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382253	0.81[ASN][1000 genomes]
rs9382254	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs9395879	0.81[AMR][1000 genomes]
rs9395880	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395882	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9395883	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9395884	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9463996	0.81[CHB][hapmap]
rs9463997	0.81[CHB][hapmap]
rs9474680	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9395887	ARID4B	trans	parietal	SCAN
rs9395887	LRRC1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
4	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
5	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
6	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:53739000-53753600	Weak transcription	NHEK	skin
8	chr6:53739000-53767800	Weak transcription	Ovary	ovary
9	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
10	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:53740400-53754000	Weak transcription	HSMM	muscle
12	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
15	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
16	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
19	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
20	chr6:53744800-53760400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:53745400-53760600	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:53746200-53757200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:53746200-53758000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:53746400-53758600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:53746400-53762000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:53746800-53762000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:53747000-53753600	Weak transcription	HMEC	breast
30	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
31	chr6:53748800-53754600	Weak transcription	HSMMtube	muscle
32	chr6:53749000-53761800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:53749200-53763600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:53749200-53765800	Weak transcription	Primary T cells from cord blood	blood
35	chr6:53749400-53762600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:53750600-53753600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:53750600-53760200	Weak transcription	HepG2	liver
38	chr6:53751600-53755400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:53751800-53754800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:53752200-53754800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:53752200-53755000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr6:53752200-53756000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr6:53752400-53754000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:53752400-53757200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:53752400-53758800	Weak transcription	Brain Angular Gyrus	brain
46	chr6:53752400-53761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:53752400-53771000	Weak transcription	Gastric	stomach
48	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:53752600-53753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:53752600-53756400	Weak transcription	Brain Substantia Nigra	brain

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