Variant report

Variant	rs3798953
Chromosome Location	chr6:161689816-161689817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161623919..161626414-chr6:161687657..161690363,2	K562	blood:
2	chr6:161688341..161690603-chr6:161735009..161737398,2	K562	blood:
3	chr6:161689546..161691232-chr6:161766488..161768941,2	K562	blood:
4	chr6:161535825..161538708-chr6:161688677..161691467,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12190239	0.82[CHB][hapmap]
rs12202278	0.82[CHB][hapmap]
rs12207275	0.82[CHB][hapmap]
rs16892376	0.83[ASN][1000 genomes]
rs34784502	0.83[ASN][1000 genomes]
rs3757033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3757038	0.83[ASN][1000 genomes]
rs3798950	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798956	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3823058	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs55977455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62437578	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62437580	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6455713	0.82[CHB][hapmap]
rs6914451	0.90[ASN][1000 genomes]
rs9458175	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9458179	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv949397	chr6:161592100-161812932	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2752091	chr6:161592100-161855785	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1029727	chr6:161607680-161814295	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1030623	chr6:161611170-161796985	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv538494	chr6:161611170-161796985	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv886818	chr6:161629323-161723705	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv533149	chr6:161653240-161769727	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1031234	chr6:161676768-162250726	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3386397	chr6:161689390-161689833	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798953	PARK2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161638200-161693800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:161649600-161693800	Weak transcription	Right Atrium	heart
3	chr6:161653800-161693800	Weak transcription	Primary B cells from cord blood	blood
4	chr6:161657600-161693600	Weak transcription	Left Ventricle	heart
5	chr6:161664800-161693800	Weak transcription	HSMM	muscle
6	chr6:161665000-161693600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:161665200-161692600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:161666400-161692600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:161666800-161694200	Weak transcription	Aorta	Aorta
10	chr6:161670800-161692600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:161672800-161694200	Weak transcription	Lung	lung
12	chr6:161672800-161694200	Weak transcription	Right Ventricle	heart
13	chr6:161674000-161692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:161676000-161693800	Weak transcription	Adipose Nuclei	Adipose
15	chr6:161676200-161694000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:161676600-161692800	Weak transcription	Fetal Lung	lung
17	chr6:161677200-161692200	Weak transcription	Spleen	Spleen
18	chr6:161677600-161690400	Weak transcription	Fetal Brain Male	brain
19	chr6:161678200-161693600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:161678600-161694200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:161678800-161693600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:161678800-161694000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:161679400-161692400	Weak transcription	Fetal Heart	heart
24	chr6:161679400-161692800	Weak transcription	NHDF-Ad	bronchial
25	chr6:161679600-161692000	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:161679800-161693600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:161680200-161693800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:161680200-161693800	Weak transcription	Small Intestine	intestine
29	chr6:161681000-161693800	Weak transcription	HMEC	breast
30	chr6:161681000-161694200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:161681200-161693200	Weak transcription	HUVEC	blood vessel
32	chr6:161681200-161693600	Weak transcription	NHLF	lung
33	chr6:161681400-161692400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:161681600-161692800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:161682200-161692200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:161682400-161692600	Weak transcription	NH-A	brain
37	chr6:161683000-161693200	Weak transcription	NHEK	skin
38	chr6:161685800-161693000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:161686200-161690600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:161686200-161693800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:161686600-161691800	Enhancers	Brain Hippocampus Middle	brain
42	chr6:161686800-161691600	Enhancers	Brain Substantia Nigra	brain
43	chr6:161687000-161691200	Enhancers	Brain Angular Gyrus	brain
44	chr6:161687200-161692600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:161687400-161690400	Weak transcription	Esophagus	oesophagus
46	chr6:161687400-161691000	Weak transcription	Fetal Brain Female	brain
47	chr6:161687600-161690400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:161687600-161692400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:161687600-161693200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:161687800-161690200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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