Variant report

Variant	rs1534555
Chromosome Location	chr4:99488312-99488313
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	chr4:99485403..99488335-chr4:99490236..99493906,4	MCF-7	breast:
2	chr4:99483863..99486365-chr4:99487741..99490347,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10002696	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10006366	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10018825	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10021234	0.84[ASN][1000 genomes]
rs10021296	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10023449	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10025051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11097622	0.80[ASN][1000 genomes]
rs13108940	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs13141997	0.92[CEU][hapmap]
rs13149070	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1358546	0.80[ASN][1000 genomes]
rs1358547	0.80[ASN][1000 genomes]
rs1528547	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1534554	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893714	0.82[JPT][hapmap]
rs1919210	0.84[ASN][1000 genomes]
rs1919211	0.81[CEU][hapmap]
rs2037832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2866016	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2866017	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes]
rs4699343	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4699344	0.83[ASN][1000 genomes]
rs4699345	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4699348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4699349	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4699353	0.82[JPT][hapmap]
rs4699354	1.00[JPT][hapmap]
rs4699639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4699640	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4699644	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs4699646	0.83[ASN][1000 genomes]
rs4699648	0.84[ASN][1000 genomes]
rs6532742	0.92[CEU][hapmap]
rs6532751	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6815038	0.83[ASN][1000 genomes]
rs6823547	0.83[ASN][1000 genomes]
rs6831643	0.92[CEU][hapmap]
rs6837359	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs71600251	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7672134	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7678323	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883619	0.80[ASN][1000 genomes]
rs9996851	0.80[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1534555	TSPAN5	cis	cerebellum	SCAN

Chromatin state (count:75 , 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	chr4:99479000-99490200	Weak transcription	HSMMtube	muscle
3	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
4	chr4:99483200-99495800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:99483400-99498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:99484200-99495400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:99485000-99490800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:99485000-99501400	Weak transcription	HUVEC	blood vessel
9	chr4:99485400-99491000	Enhancers	Fetal Brain Male	brain
10	chr4:99485400-99495000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:99485600-99488400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:99485600-99489200	Enhancers	Fetal Heart	heart
13	chr4:99485800-99488400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr4:99486000-99488400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:99486000-99488400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:99486000-99488400	Enhancers	Rectal Smooth Muscle	rectum
17	chr4:99486000-99488800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:99486000-99489000	Enhancers	Ovary	ovary
19	chr4:99486000-99489200	Enhancers	Fetal Thymus	thymus
20	chr4:99486000-99491000	Enhancers	Thymus	Thymus
21	chr4:99486000-99491400	Enhancers	Fetal Muscle Leg	muscle
22	chr4:99486600-99488600	Enhancers	Fetal Stomach	stomach
23	chr4:99486800-99488400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:99486800-99488400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:99486800-99488400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr4:99486800-99488400	Enhancers	Fetal Lung	lung
27	chr4:99486800-99488400	Enhancers	Left Ventricle	heart
28	chr4:99487000-99488400	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr4:99487000-99488800	Enhancers	NHDF-Ad	bronchial
30	chr4:99487200-99500000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:99487400-99495000	Weak transcription	Primary T cells from cord blood	blood
32	chr4:99487600-99488400	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr4:99487600-99488400	Enhancers	NH-A	brain
34	chr4:99487600-99490200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:99487600-99492200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:99487800-99488400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:99487800-99488400	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr4:99487800-99488400	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr4:99487800-99490000	Weak transcription	Fetal Kidney	kidney
40	chr4:99487800-99490000	Weak transcription	Osteobl	bone
41	chr4:99487800-99491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:99487800-99492200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:99487800-99498600	Weak transcription	NHLF	lung
44	chr4:99488000-99488400	Enhancers	Colon Smooth Muscle	Colon
45	chr4:99488000-99490000	Weak transcription	Esophagus	oesophagus
46	chr4:99488000-99490000	Weak transcription	Fetal Intestine Large	intestine
47	chr4:99488000-99492000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:99488000-99492600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:99488000-99495200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:99488000-99495200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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