Variant report

Variant	rs735117
Chromosome Location	chr6:38141022-38141023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38140845..38143617-chr6:38230207..38231726,2	MCF-7	breast:
2	chr6:38137479..38141029-chr6:38143334..38147856,5	K562	blood:
3	chr6:38137479..38141029-chr6:38144999..38147856,3	K562	blood:
4	chr6:38129827..38133473-chr6:38138909..38141756,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10807190	0.85[JPT][hapmap]
rs10807191	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs10807192	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs10947713	0.89[CHB][hapmap]
rs10947714	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs10947716	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11754110	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11756830	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12196879	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12197001	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12198616	0.82[CHB][hapmap]
rs12206712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13205068	0.81[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs13212638	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17678747	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[YRI][hapmap]
rs2092426	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2143403	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs2235711	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs3800358	0.80[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs3823431	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6458041	0.81[CHB][hapmap]
rs6458044	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6938410	0.98[EUR][1000 genomes]
rs71544417	0.82[AMR][1000 genomes]
rs71556980	0.86[ASN][1000 genomes]
rs737171	0.83[ASN][1000 genomes]
rs742537	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs742538	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs742539	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs761153	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7742915	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs7756835	0.81[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs909998	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926565	0.90[CHB][hapmap]
rs9462404	0.86[JPT][hapmap]
rs9462405	0.90[CHB][hapmap]
rs9462409	0.90[CHB][hapmap]
rs9470806	0.94[ASN][1000 genomes]
rs9470807	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9470811	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs9470813	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs9470816	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470818	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470822	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470823	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470824	0.88[EUR][1000 genomes]
rs9470825	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription 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	26 gene(s)	inside rSNPs	diseases
6	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv524213	chr6:38106844-38160627	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv517973	chr6:38131442-38152460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
9	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs735117	GLO1	cis	parietal	SCAN
rs735117	STK38	cis	cerebellum	SCAN
rs735117	C6orf126	cis	parietal	SCAN
rs735117	CDKN1A	cis	cerebellum	SCAN
rs735117	ZFAND3	cis	cerebellum	SCAN
rs735117	KCTD20	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38091400-38141800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:38121000-38159600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38121800-38153600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:38123200-38153200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:38123400-38155400	Weak transcription	Aorta	Aorta
6	chr6:38123400-38157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:38123600-38144200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:38123600-38153000	Weak transcription	Primary B cells from cord blood	blood
10	chr6:38123800-38141400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:38123800-38151200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:38124000-38152200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:38124200-38151800	Weak transcription	Brain Anterior Caudate	brain
14	chr6:38124400-38144200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:38129200-38145600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:38129400-38141200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:38129400-38141200	Weak transcription	Lung	lung
18	chr6:38129400-38144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:38129600-38141200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:38130000-38144400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:38130600-38141200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:38131200-38143800	Weak transcription	Thymus	Thymus
23	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
24	chr6:38132600-38141200	Weak transcription	Ovary	ovary
25	chr6:38133600-38144600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:38133600-38160400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:38136000-38159800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:38136800-38145200	Genic enhancers	Fetal Intestine Small	intestine
30	chr6:38136800-38156000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:38137200-38143000	Enhancers	Fetal Intestine Large	intestine
32	chr6:38137600-38141400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr6:38137600-38141400	Weak transcription	Right Ventricle	heart
34	chr6:38137600-38144200	Strong transcription	Spleen	Spleen
35	chr6:38138200-38142200	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:38138200-38142600	Weak transcription	Gastric	stomach
37	chr6:38138200-38143600	Weak transcription	Esophagus	oesophagus
38	chr6:38138200-38147200	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:38138400-38141400	Weak transcription	Brain Substantia Nigra	brain
40	chr6:38138400-38143800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:38138400-38144400	Weak transcription	Pancreas	Pancrea
42	chr6:38138400-38145200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:38138400-38145400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:38138400-38147200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:38138400-38147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:38138600-38141400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:38138600-38145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:38138800-38141200	Enhancers	Liver	Liver
50	chr6:38138800-38143400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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