Variant report

Variant	rs820089
Chromosome Location	chr6:35024695-35024696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35020203..35022159-chr6:35023011..35024992,4	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1093985	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947537	0.81[GIH][hapmap]
rs12661389	0.81[GIH][hapmap]
rs13191889	0.86[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1535815	0.81[GIH][hapmap]
rs1568705	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16896390	0.81[JPT][hapmap]
rs16896553	0.91[JPT][hapmap]
rs2049316	0.90[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2140420	0.81[CEU][hapmap]
rs2689091	0.81[GIH][hapmap]
rs2689097	0.80[EUR][1000 genomes]
rs2762342	0.82[EUR][1000 genomes]
rs2762343	0.81[GIH][hapmap]
rs2762350	0.81[CEU][hapmap]
rs2820224	0.88[ASN][1000 genomes]
rs2820229	0.81[CEU][hapmap]
rs2820230	0.94[ASN][1000 genomes]
rs3800424	0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3800426	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3800430	0.91[JPT][hapmap]
rs3800433	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3823437	0.81[ASN][1000 genomes]
rs6937805	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs707967	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72537461	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820068	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820073	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820074	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820075	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820078	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820079	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820080	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820081	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820084	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820087	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820088	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820091	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs820092	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820093	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs820094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820096	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs820097	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs820098	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs865353	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357193	0.89[JPT][hapmap]
rs9469933	0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs820089	ANKS1A	cis	cerebellum	SCAN
rs820089	ANKS1A	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34994600-35036000	Weak transcription	K562	blood
2	chr6:35015800-35044200	Weak transcription	HMEC	breast
3	chr6:35016200-35055000	Weak transcription	Hela-S3	cervix
4	chr6:35016800-35026400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:35016800-35026800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:35016800-35027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:35016800-35028000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:35016800-35028000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:35017000-35026000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:35017000-35026200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:35017000-35026200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:35017400-35028000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:35017400-35028600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:35017600-35028000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:35017600-35036200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:35017800-35024800	Weak transcription	Fetal Heart	heart
17	chr6:35017800-35027600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:35017800-35053000	Weak transcription	Small Intestine	intestine
19	chr6:35018200-35025400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:35018200-35025600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:35018400-35052800	Weak transcription	Fetal Kidney	kidney
22	chr6:35018600-35025000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:35018600-35027800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:35018600-35051000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr6:35018800-35026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:35018800-35029000	Weak transcription	NHDF-Ad	bronchial
27	chr6:35018800-35038200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr6:35018800-35060600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:35019400-35027600	Weak transcription	Dnd41	blood
30	chr6:35020000-35025200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:35020000-35059800	Strong transcription	Fetal Intestine Small	intestine
32	chr6:35020200-35037600	Strong transcription	Fetal Intestine Large	intestine
33	chr6:35020400-35059400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:35020600-35034800	Strong transcription	Primary T cells from cord blood	blood
35	chr6:35020800-35025000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:35021000-35037000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr6:35021000-35037600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr6:35021200-35025400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:35021200-35025800	Weak transcription	Fetal Brain Female	brain
40	chr6:35021200-35026800	Weak transcription	Psoas Muscle	Psoas
41	chr6:35021200-35027400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr6:35021200-35028000	Weak transcription	NHLF	lung
43	chr6:35021200-35028600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:35021200-35034800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:35021400-35025600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:35021400-35025600	Strong transcription	Fetal Lung	lung
47	chr6:35021400-35036200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:35021400-35037400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:35021600-35025200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:35021600-35025200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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