Variant report

Variant	rs6532751
Chromosome Location	chr4:99497545-99497546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99496585..99499120-chr4:99503712..99505800,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10002696	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10006366	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10018825	0.84[CHB][hapmap]
rs10021234	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10021296	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs10023449	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10025051	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10029405	0.89[ASN][1000 genomes]
rs11097622	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11940430	0.92[ASN][1000 genomes]
rs13108940	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs13149070	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs1358546	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358547	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534554	0.80[ASN][1000 genomes]
rs1534555	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1573478	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1893713	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1893714	0.82[JPT][hapmap]
rs2037832	0.89[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2866016	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2866017	0.84[CHB][hapmap]
rs4699343	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4699345	0.89[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs4699348	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4699349	1.00[JPT][hapmap]
rs4699353	0.87[JPT][hapmap]
rs4699354	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4699639	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4699640	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs6844261	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs7672134	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs7678323	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs883619	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996851	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6532751	TSPAN5	cis	cerebellum	SCAN
rs6532751	MIR623	trans	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
3	chr4:99483400-99498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:99485000-99501400	Weak transcription	HUVEC	blood vessel
5	chr4:99487200-99500000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:99487800-99498600	Weak transcription	NHLF	lung
7	chr4:99488000-99499000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:99488000-99499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:99488200-99500200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:99489000-99498800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:99490200-99499000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:99490400-99499200	Weak transcription	Brain Germinal Matrix	brain
13	chr4:99490600-99498600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:99490600-99498800	Weak transcription	Stomach Mucosa	stomach
15	chr4:99490600-99501400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:99490800-99499600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:99490800-99499800	Weak transcription	Right Atrium	heart
18	chr4:99490800-99506600	Weak transcription	Esophagus	oesophagus
19	chr4:99490800-99509000	Weak transcription	HSMM	muscle
20	chr4:99491000-99503400	Weak transcription	Thymus	Thymus
21	chr4:99492000-99498600	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:99492000-99499200	Weak transcription	Osteobl	bone
23	chr4:99492400-99498800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:99492600-99498600	Weak transcription	Brain Anterior Caudate	brain
25	chr4:99492600-99499800	Weak transcription	Spleen	Spleen
26	chr4:99492600-99500200	Weak transcription	Fetal Brain Female	brain
27	chr4:99492600-99501800	Weak transcription	Primary B cells from cord blood	blood
28	chr4:99492800-99497800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:99493200-99501400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:99493600-99498800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:99493600-99500400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:99493600-99501400	Weak transcription	Fetal Thymus	thymus
33	chr4:99493800-99498800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:99494000-99499200	Weak transcription	Fetal Lung	lung
35	chr4:99494200-99498600	Weak transcription	Brain Angular Gyrus	brain
36	chr4:99494200-99498600	Weak transcription	Brain Substantia Nigra	brain
37	chr4:99495200-99498600	Weak transcription	Fetal Kidney	kidney
38	chr4:99495200-99500200	Weak transcription	HMEC	breast
39	chr4:99495600-99498600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:99495800-99498600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:99495800-99498600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:99495800-99498600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:99495800-99499000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:99495800-99499800	Weak transcription	NHEK	skin
45	chr4:99496000-99498800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:99496000-99499000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:99496000-99502000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:99496000-99502000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:99496200-99498000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr4:99496200-99498400	Weak transcription	Brain Cingulate Gyrus	brain

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