Variant report

Variant	rs12508322
Chromosome Location	chr4:99403566-99403567
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	chr4:99402389..99404917-chr4:99406688..99409637,2	K562	blood:
2	chr4:99180371..99183647-chr4:99401160..99403823,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214559	Chromatin interaction
ENSG00000138698	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10001086	0.85[CHB][hapmap]
rs10002767	0.85[CHB][hapmap]
rs10003517	0.82[CHB][hapmap]
rs10003618	0.85[CHB][hapmap]
rs10005811	0.82[CHB][hapmap]
rs10014034	0.85[CHB][hapmap]
rs10017792	0.86[ASN][1000 genomes]
rs10022047	0.82[CHB][hapmap]
rs10028275	0.82[CHB][hapmap]
rs10028373	0.82[CHB][hapmap]
rs10030765	0.88[ASN][1000 genomes]
rs10032440	0.85[CHB][hapmap]
rs10516429	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs10516431	0.85[CHB][hapmap]
rs12498745	0.82[CHB][hapmap]
rs12499136	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12501972	0.86[ASN][1000 genomes]
rs12501974	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12503056	0.86[ASN][1000 genomes]
rs12503806	0.85[CHB][hapmap]
rs12505246	0.82[CHB][hapmap]
rs12507118	0.85[CHB][hapmap]
rs12507425	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12507859	0.85[CHB][hapmap]
rs12509125	0.82[CHB][hapmap]
rs12509417	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12509834	0.85[CHB][hapmap]
rs12510055	0.82[CHB][hapmap]
rs12512920	0.82[CHB][hapmap]
rs13353584	0.85[CHB][hapmap]
rs1399242	0.82[CHB][hapmap]
rs1399243	0.82[CHB][hapmap]
rs1580065	0.82[CHB][hapmap]
rs17027449	0.85[CHB][hapmap]
rs17027452	0.82[CHB][hapmap]
rs17027530	1.00[CHB][hapmap]
rs17027532	0.85[CHB][hapmap]
rs17027533	0.82[CHB][hapmap]
rs17027543	0.82[CHB][hapmap]
rs17027545	0.85[CHB][hapmap]
rs17027549	0.85[CHB][hapmap]
rs17027552	0.82[CHB][hapmap]
rs17027564	0.82[CHB][hapmap]
rs17027585	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs17027603	0.88[ASN][1000 genomes]
rs1913488	0.86[ASN][1000 genomes]
rs1913489	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs1913490	0.85[CHB][hapmap]
rs2081490	0.85[CHB][hapmap]
rs2090118	0.88[ASN][1000 genomes]
rs28416087	0.86[ASN][1000 genomes]
rs28568441	0.88[ASN][1000 genomes]
rs28733733	0.88[ASN][1000 genomes]
rs28798461	0.88[ASN][1000 genomes]
rs3775537	0.82[CHB][hapmap]
rs3775538	0.85[CHB][hapmap]
rs3822115	0.85[CHB][hapmap]
rs4699622	0.82[CHB][hapmap]
rs4699623	0.85[CHB][hapmap]
rs4699626	0.82[CHB][hapmap]
rs4699627	0.85[CHB][hapmap]
rs4699628	0.82[CHB][hapmap]
rs4699629	0.85[CHB][hapmap]
rs4699630	0.85[CHB][hapmap]
rs4699632	0.85[CHB][hapmap]
rs4699634	0.82[CHB][hapmap]
rs6532732	0.82[CHB][hapmap]
rs6822914	0.85[CHB][hapmap]
rs6828936	0.82[CHB][hapmap]
rs6831490	0.85[CHB][hapmap]
rs6831730	0.82[CHB][hapmap]
rs6833504	0.82[CHB][hapmap]
rs6834829	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs6835411	0.82[CHB][hapmap]
rs6835676	0.88[ASN][1000 genomes]
rs6845766	0.86[ASN][1000 genomes]
rs6846417	0.82[CHB][hapmap]
rs72688435	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs72688437	0.83[AMR][1000 genomes]
rs73832309	0.86[ASN][1000 genomes]
rs7654497	0.82[CHB][hapmap]
rs7655147	0.85[CHB][hapmap]
rs7655427	0.85[CHB][hapmap]
rs7656017	0.85[CHB][hapmap]
rs7664210	0.86[ASN][1000 genomes]
rs7673119	0.82[CHB][hapmap]
rs7675605	0.89[ASN][1000 genomes]
rs7676060	0.85[CHB][hapmap]
rs7676285	0.86[ASN][1000 genomes]
rs7683964	0.85[CHB][hapmap]
rs7687685	0.82[CHB][hapmap]
rs7694221	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs890207	0.85[CHB][hapmap]
rs919027	0.82[CHB][hapmap]
rs9992518	0.82[CHB][hapmap]

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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99389200-99403600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr4:99389200-99404000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:99389200-99404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:99389200-99404000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:99389200-99404200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:99389200-99407000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:99389200-99413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:99389400-99403800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:99389400-99419800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:99390000-99405000	Weak transcription	Fetal Intestine Small	intestine
11	chr4:99390200-99404000	Weak transcription	Spleen	Spleen
12	chr4:99390200-99404200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:99390200-99405400	Weak transcription	Left Ventricle	heart
14	chr4:99390800-99413200	Weak transcription	Brain Anterior Caudate	brain
15	chr4:99392000-99404600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:99392600-99403600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:99392600-99408600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:99392600-99411800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:99394000-99413200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:99396200-99431400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:99396400-99412400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:99397600-99439400	Weak transcription	Primary B cells from cord blood	blood
23	chr4:99398000-99407600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:99398800-99403800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:99399600-99404000	Weak transcription	Thymus	Thymus
26	chr4:99399600-99407600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:99400000-99404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:99400000-99406000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:99400000-99406000	Enhancers	HMEC	breast
30	chr4:99400000-99406200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:99400000-99406400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:99400000-99412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:99400000-99429800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:99400200-99403800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:99400200-99404000	Weak transcription	NHLF	lung
36	chr4:99400200-99407200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:99400200-99411200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:99400400-99419200	Weak transcription	Fetal Thymus	thymus
39	chr4:99400600-99404200	Genic enhancers	NHDF-Ad	bronchial
40	chr4:99401200-99404200	Enhancers	Brain Substantia Nigra	brain
41	chr4:99401400-99403800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:99401600-99404000	Enhancers	Brain Hippocampus Middle	brain
43	chr4:99401600-99406600	Enhancers	Stomach Mucosa	stomach
44	chr4:99401800-99404000	Enhancers	Fetal Lung	lung
45	chr4:99401800-99404600	Enhancers	Brain Angular Gyrus	brain
46	chr4:99401800-99404600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr4:99402000-99404800	Enhancers	Ovary	ovary
48	chr4:99402200-99404200	Weak transcription	Esophagus	oesophagus
49	chr4:99402200-99404200	Weak transcription	Gastric	stomach
50	chr4:99402400-99404000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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