Variant report

Variant	rs10003332
Chromosome Location	chr4:87895221-87895222
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87892815..87895496-chr4:87897060..87900132,4	MCF-7	breast:
2	chr4:87894083..87901163-chr4:87926378..87930735,13	K562	blood:
3	chr4:87885535..87895894-chr4:87923652..87929924,15	K562	blood:
4	chr4:87856296..87858814-chr4:87892568..87895744,3	MCF-7	breast:
5	chr4:87892847..87896142-chr4:87913687..87916404,3	K562	blood:
6	chr4:87894580..87900721-chr4:87926553..87929375,8	MCF-7	breast:
7	chr4:87876640..87879559-chr4:87894378..87897359,2	K562	blood:
8	chr4:87891928..87895544-chr4:87897508..87902479,6	K562	blood:
9	chr4:87854105..87855852-chr4:87892879..87895609,2	K562	blood:
10	chr4:87858518..87860018-chr4:87894461..87896898,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10008600	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10022960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13119324	0.80[ASN][1000 genomes]
rs1374936	0.91[ASN][1000 genomes]
rs1374937	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1584345	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs168161	0.92[ASN][1000 genomes]
rs17012291	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1868245	0.80[ASN][1000 genomes]
rs1972969	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs2053772	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2053774	0.99[ASN][1000 genomes]
rs2272777	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2594276	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs2594280	0.82[AFR][1000 genomes]
rs2705617	0.91[ASN][1000 genomes]
rs340627	0.89[ASN][1000 genomes]
rs340628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs340629	0.89[ASN][1000 genomes]
rs340631	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs340632	0.88[ASN][1000 genomes]
rs340635	0.92[ASN][1000 genomes]
rs340640	0.89[ASN][1000 genomes]
rs340644	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs340645	0.89[ASN][1000 genomes]
rs340646	0.84[ASN][1000 genomes]
rs340647	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs340649	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs340652	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4536897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4693155	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4693797	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4693799	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs58317309	0.85[ASN][1000 genomes]
rs6531943	0.95[ASN][1000 genomes]
rs6531944	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6531945	0.91[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs6531947	0.89[ASN][1000 genomes]
rs6815546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6848056	0.85[ASN][1000 genomes]
rs6853011	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73837575	0.89[ASN][1000 genomes]
rs7685248	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs895740	0.91[ASN][1000 genomes]
rs965824	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]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
rs10003332	Hs.480174	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87868600-87898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:87881000-87897600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:87882000-87895400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:87882200-87895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:87882400-87898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:87886600-87898600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:87888200-87895800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:87888800-87898800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:87889200-87895400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:87890200-87898600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:87891200-87896200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:87891400-87896000	Enhancers	Stomach Mucosa	stomach
16	chr4:87891600-87897600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:87891800-87895400	Enhancers	K562	blood
18	chr4:87891800-87895600	Enhancers	Fetal Thymus	thymus
19	chr4:87892000-87900400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:87892200-87907000	Weak transcription	Brain Anterior Caudate	brain
21	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:87892600-87896600	Enhancers	Dnd41	blood
23	chr4:87892600-87898400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:87892800-87898600	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:87892800-87909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:87893200-87896400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:87893200-87900200	Weak transcription	Esophagus	oesophagus
28	chr4:87893400-87895600	Enhancers	Duodenum Mucosa	Duodenum
29	chr4:87893400-87895800	Enhancers	Fetal Intestine Large	intestine
30	chr4:87893800-87895400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr4:87893800-87895600	Flanking Active TSS	HepG2	liver
32	chr4:87893800-87896200	Enhancers	Primary hematopoietic stem cells	blood
33	chr4:87893800-87896600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:87894000-87895400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr4:87894000-87895400	Enhancers	Fetal Intestine Small	intestine
36	chr4:87894000-87895400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr4:87894000-87895600	Enhancers	NHEK	skin
38	chr4:87894000-87895800	Enhancers	Thymus	Thymus
39	chr4:87894000-87896000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:87894000-87896400	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr4:87894200-87895400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:87894200-87895600	Enhancers	Small Intestine	intestine
43	chr4:87894200-87895800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:87894200-87897800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr4:87894200-87899000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr4:87894400-87897400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:87894400-87897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:87894400-87898400	Weak transcription	Osteobl	bone
49	chr4:87894400-87898600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr4:87894400-87898600	Weak transcription	Rectal Smooth Muscle	rectum

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