Variant report

Variant	rs965824
Chromosome Location	chr4:87880096-87880097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87875765..87890159-chr4:87922878..87933002,25	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10008600	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10022960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1374936	0.88[ASN][1000 genomes]
rs1374937	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1584345	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs168161	0.89[ASN][1000 genomes]
rs17012291	0.91[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs1972969	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs2053772	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2053774	0.96[ASN][1000 genomes]
rs2272777	0.91[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs2594276	0.92[CHB][hapmap]
rs2594280	0.84[AFR][1000 genomes]
rs2705617	0.88[ASN][1000 genomes]
rs340627	0.87[ASN][1000 genomes]
rs340628	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs340629	0.87[ASN][1000 genomes]
rs340631	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs340632	0.86[ASN][1000 genomes]
rs340635	0.89[ASN][1000 genomes]
rs340640	0.87[ASN][1000 genomes]
rs340644	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs340645	0.87[ASN][1000 genomes]
rs340646	0.81[ASN][1000 genomes]
rs340647	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs340649	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs340652	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4536897	0.90[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4693155	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4693797	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4693799	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs58317309	0.83[ASN][1000 genomes]
rs6531943	0.92[ASN][1000 genomes]
rs6531944	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6531945	0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs6531947	0.87[ASN][1000 genomes]
rs6815546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6848056	0.82[ASN][1000 genomes]
rs6853011	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73837575	0.87[ASN][1000 genomes]
rs7685248	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs895740	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs965824	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87857600-87882000	Weak transcription	Spleen	Spleen
2	chr4:87857800-87880200	Weak transcription	HSMM	muscle
3	chr4:87858600-87881000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87861400-87880800	Weak transcription	Aorta	Aorta
5	chr4:87861800-87880600	Weak transcription	Fetal Kidney	kidney
6	chr4:87864400-87880600	Weak transcription	Gastric	stomach
7	chr4:87864400-87880800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:87868200-87880600	Weak transcription	Lung	lung
9	chr4:87868200-87881200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:87868400-87880800	Weak transcription	Pancreas	Pancrea
11	chr4:87868400-87881400	Weak transcription	Colonic Mucosa	Colon
12	chr4:87868400-87891800	Weak transcription	Esophagus	oesophagus
13	chr4:87868600-87886800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:87868600-87898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:87869000-87880800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:87869400-87881800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:87869600-87881200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:87869600-87882000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:87869600-87886200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:87869800-87880600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:87869800-87880800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:87869800-87880800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:87869800-87888000	Weak transcription	HUVEC	blood vessel
24	chr4:87869800-87894000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:87870200-87880600	Weak transcription	Brain Substantia Nigra	brain
26	chr4:87870200-87880800	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:87871600-87881800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:87872000-87880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:87872000-87881800	Weak transcription	Ovary	ovary
30	chr4:87872400-87880800	Weak transcription	Left Ventricle	heart
31	chr4:87872400-87880800	Weak transcription	Right Ventricle	heart
32	chr4:87872400-87882000	Weak transcription	Primary T cells from cord blood	blood
33	chr4:87872600-87880200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:87872600-87880800	Weak transcription	Psoas Muscle	Psoas
35	chr4:87872600-87881200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:87872600-87882800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:87872800-87891400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:87875200-87882400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:87875600-87882000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:87876000-87880200	Weak transcription	Fetal Intestine Large	intestine
42	chr4:87876600-87880600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:87876600-87886400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:87877000-87881800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:87877400-87886200	Weak transcription	Hela-S3	cervix
46	chr4:87877600-87881400	Weak transcription	A549	lung
47	chr4:87877600-87882800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:87878000-87883400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr4:87878400-87880800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:87878400-87881800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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