Variant report

Variant	rs9838117
Chromosome Location	chr3:178952507-178952508
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178945435..178949746-chr3:178950084..178953844,5	K562	blood:
2	chr3:178951996..178954548-chr3:178958414..178959970,2	K562	blood:
3	chr3:178951419..178954730-chr3:178963879..178966667,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11919383	0.87[CEU][hapmap]
rs12488074	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1970901	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs3729674	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs3729676	0.94[CEU][hapmap]
rs3975510	0.81[EUR][1000 genomes]
rs3975513	0.81[EUR][1000 genomes]
rs3976507	0.87[CEU][hapmap]
rs4855093	0.81[CEU][hapmap]
rs4855095	0.87[CEU][hapmap]
rs6443619	0.87[CEU][hapmap]
rs6443625	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6767284	0.87[CEU][hapmap]
rs6769154	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6769162	0.81[EUR][1000 genomes]
rs6769508	0.87[CEU][hapmap]
rs6782557	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6786114	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6798817	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6803219	0.81[EUR][1000 genomes]
rs6806917	0.87[CEU][hapmap]
rs6810246	0.87[CEU][hapmap]
rs7614305	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7615076	0.87[CEU][hapmap]
rs7621329	0.87[CEU][hapmap]
rs7621436	0.87[CEU][hapmap]
rs7623154	0.87[CEU][hapmap]
rs7635669	0.81[CEU][hapmap]
rs7636454	0.87[CEU][hapmap]
rs7638323	0.87[CEU][hapmap]
rs7641983	0.87[CEU][hapmap]
rs7644648	0.87[CEU][hapmap]
rs7646409	0.87[CEU][hapmap]
rs9813190	0.81[CEU][hapmap]
rs9829903	0.94[CEU][hapmap]
rs9831234	0.87[CEU][hapmap]
rs9838411	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv878038	chr3:178924867-178962897	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878039	chr3:178933363-178968568	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv965236	chr3:178938931-178955061	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9838117	SOX2	cis	parietal	SCAN
rs9838117	C2orf69	trans	parietal	SCAN
rs9838117	USP13	cis	cerebellum	SCAN
rs9838117	KCNMB3	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178906400-178962400	Weak transcription	HepG2	liver
2	chr3:178911200-178953400	Weak transcription	Gastric	stomach
3	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
4	chr3:178913800-178954000	Weak transcription	Fetal Heart	heart
5	chr3:178913800-178969000	Weak transcription	Small Intestine	intestine
6	chr3:178914800-178972800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:178915800-178965200	Weak transcription	Hela-S3	cervix
8	chr3:178917600-178953800	Weak transcription	Colonic Mucosa	Colon
9	chr3:178920200-178952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:178920200-178968400	Weak transcription	Spleen	Spleen
11	chr3:178925800-178968200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:178925800-178968600	Weak transcription	Pancreas	Pancrea
13	chr3:178928600-178962400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:178928800-178953200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:178929200-178954000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:178929800-178962800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:178930600-178954200	Weak transcription	Fetal Intestine Small	intestine
18	chr3:178932200-178974000	Weak transcription	Lung	lung
19	chr3:178938800-178954000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:178941800-178972600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:178942800-178965400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:178945600-178953000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:178945800-178978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:178946800-178953400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:178946800-178953800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:178947000-178952800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:178947000-178954200	Strong transcription	Fetal Thymus	thymus
28	chr3:178947400-178952800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:178947800-178953600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:178947800-178953800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:178948000-178954000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:178948200-178955000	Weak transcription	HMEC	breast
33	chr3:178948200-178967400	Weak transcription	NHDF-Ad	bronchial
34	chr3:178948400-178967600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:178948800-178962200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:178948800-178966600	Weak transcription	Psoas Muscle	Psoas
37	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:178949000-178953600	Weak transcription	Esophagus	oesophagus
39	chr3:178949000-178953800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:178949000-178954200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:178949000-178954200	Weak transcription	Fetal Brain Male	brain
42	chr3:178949000-178962600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:178949000-178962800	Weak transcription	Left Ventricle	heart
44	chr3:178949000-178964400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:178949000-178966200	Weak transcription	Aorta	Aorta
46	chr3:178949000-178968200	Weak transcription	Fetal Stomach	stomach
47	chr3:178949000-178970800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:178949000-178978200	Weak transcription	NHLF	lung
49	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:178949000-178978600	Weak transcription	Ovary	ovary

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