Variant report

Variant	rs2820232
Chromosome Location	chr6:35003603-35003604
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35002561..35006786-chr6:35010332..35014287,4	K562	blood:
2	chr6:34998385..35000765-chr6:35002872..35004521,2	MCF-7	breast:
3	chr6:35002495..35005140-chr6:35015377..35017563,2	K562	blood:
4	chr6:34994556..34998578-chr6:34998827..35004744,6	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10947537	1.00[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap]
rs12525532	0.85[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[MKK][hapmap];0.87[ASN][1000 genomes]
rs12661389	1.00[ASW][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap]
rs13210323	0.84[CHD][hapmap]
rs1535001	0.90[JPT][hapmap]
rs1535815	1.00[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs1996912	0.82[JPT][hapmap]
rs2257663	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs2494099	0.81[ASN][1000 genomes]
rs2494100	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs2689091	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs2689094	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2762335	0.94[ASN][1000 genomes]
rs2762337	0.90[ASN][1000 genomes]
rs2762343	0.83[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap]
rs2762345	0.96[ASN][1000 genomes]
rs2820223	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2820226	0.88[ASN][1000 genomes]
rs2820228	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs2820233	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2820234	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2820237	0.90[JPT][hapmap]
rs3817473	0.90[JPT][hapmap]
rs3823438	1.00[JPT][hapmap];1.00[MKK][hapmap]
rs4646949	0.81[JPT][hapmap]
rs847846	0.85[JPT][hapmap]
rs847850	0.95[JPT][hapmap]
rs847851	0.90[JPT][hapmap]
rs847852	1.00[ASW][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap]
rs847858	0.94[JPT][hapmap]
rs847859	0.90[JPT][hapmap]
rs9380469	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2820232	TAF11	cis	cerebellum	SCAN
rs2820232	RBPMS	trans	lymphoblastoid	seeQTL
rs2820232	C6orf227	cis	cerebellum	SCAN
rs2820232	FXYD2	trans	lymphoblastoid	seeQTL
rs2820232	NDUFAF1	cis	Temporal Cortex	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:34963600-35006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:34986200-35015000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:34986400-35011800	Weak transcription	Dnd41	blood
5	chr6:34986800-35014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:34987000-35009000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:34987000-35015800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:34987400-35015800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:34992800-35011800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:34993800-35006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:34993800-35014600	Weak transcription	Fetal Brain Male	brain
12	chr6:34994200-35004000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:34994200-35014400	Weak transcription	NHLF	lung
14	chr6:34994400-35005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:34994600-35036000	Weak transcription	K562	blood
16	chr6:34995000-35005600	Weak transcription	Osteobl	bone
17	chr6:34995000-35005800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:34995000-35013800	Weak transcription	Hela-S3	cervix
19	chr6:34995600-35003800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:34996000-35015200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:34996200-35005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:34996200-35010000	Weak transcription	Ovary	ovary
23	chr6:34997800-35004800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:34998600-35008000	Weak transcription	Brain Angular Gyrus	brain
25	chr6:34998800-35004400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:34999000-35005600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr6:34999000-35008600	Weak transcription	Primary B cells from cord blood	blood
28	chr6:34999400-35007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:34999800-35005000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:34999800-35007400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:34999800-35014600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:35000200-35003800	Enhancers	Fetal Heart	heart
33	chr6:35000200-35003800	Weak transcription	Fetal Kidney	kidney
34	chr6:35000200-35004800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:35000200-35005600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:35000600-35008200	Weak transcription	HepG2	liver
37	chr6:35001000-35004600	Enhancers	Brain Anterior Caudate	brain
38	chr6:35001000-35005600	Genic enhancers	HSMMtube	muscle
39	chr6:35001000-35005800	Enhancers	Aorta	Aorta
40	chr6:35001400-35004200	Genic enhancers	Left Ventricle	heart
41	chr6:35001400-35004200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr6:35001400-35005800	Enhancers	Right Ventricle	heart
43	chr6:35001600-35003800	Enhancers	Gastric	stomach
44	chr6:35001600-35004400	Enhancers	Stomach Mucosa	stomach
45	chr6:35001600-35004400	Enhancers	HUVEC	blood vessel
46	chr6:35001600-35004600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr6:35001600-35004800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:35001600-35005400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr6:35001600-35006000	Enhancers	Right Atrium	heart
50	chr6:35001800-35004200	Enhancers	Spleen	Spleen

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