Variant report

Variant	rs12640075
Chromosome Location	chr4:79533905-79533906
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79531023..79534724-chr4:79692809..79696400,3	K562	blood:
2	chr20:47236758..47237590-chr4:79533418..79534263,2	MCF-7	breast:
3	chr4:79533816..79536159-chr4:79571823..79573589,2	K562	blood:
4	chr4:79527063..79529896-chr4:79532184..79534959,3	K562	blood:
5	chr4:79508043..79510860-chr4:79533218..79535822,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1042515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725235	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11727844	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11728517	0.86[ASN][1000 genomes]
rs11736376	0.81[YRI][hapmap]
rs17003396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628566	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382063	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs56023152	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57415147	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57896096	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58089913	0.84[ASN][1000 genomes]
rs59133103	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5942	0.82[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs5950	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67280698	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817792	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819559	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836185	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837823	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72607862	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607863	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607864	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607865	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72607866	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661370	0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7668240	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7671564	0.81[YRI][hapmap]
rs7672903	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7686273	0.93[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7694152	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12640075	RP11-792D21.2	cis	Whole Blood	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:79491800-79542600	Weak transcription	NH-A	brain
3	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:79513800-79534200	Strong transcription	NHEK	skin
6	chr4:79517200-79534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
9	chr4:79521400-79534000	Weak transcription	Right Ventricle	heart
10	chr4:79524200-79543400	Weak transcription	A549	lung
11	chr4:79524400-79534000	Weak transcription	Placenta	Placenta
12	chr4:79527800-79534000	Weak transcription	Spleen	Spleen
13	chr4:79527800-79534800	Weak transcription	Gastric	stomach
14	chr4:79527800-79535200	Weak transcription	Left Ventricle	heart
15	chr4:79527800-79535200	Weak transcription	Lung	lung
16	chr4:79527800-79535400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:79528000-79534800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:79528400-79534800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:79528800-79534000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:79529400-79537600	Enhancers	Dnd41	blood
23	chr4:79529800-79536200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:79529800-79537000	Enhancers	Primary hematopoietic stem cells	blood
25	chr4:79530000-79540000	Enhancers	Primary T cells from cord blood	blood
26	chr4:79531000-79535400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr4:79531200-79536600	Enhancers	Primary B cells from cord blood	blood
28	chr4:79531200-79536800	Enhancers	Primary B cells from peripheral blood	blood
29	chr4:79531400-79543000	Weak transcription	Hela-S3	cervix
30	chr4:79531800-79543200	Weak transcription	HUVEC	blood vessel
31	chr4:79532000-79534200	Strong transcription	HMEC	breast
32	chr4:79532000-79534600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:79532000-79536800	Enhancers	Fetal Thymus	thymus
34	chr4:79532000-79537200	Weak transcription	HSMM	muscle
35	chr4:79532200-79534000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr4:79532200-79534000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:79532200-79534600	Enhancers	K562	blood
38	chr4:79532200-79535000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr4:79532200-79535200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:79532400-79534000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr4:79532400-79534000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:79532400-79534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr4:79532400-79536800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:79532400-79537200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:79532400-79537200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:79532600-79534600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:79532600-79534800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:79532600-79534800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:79532600-79535200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:79532600-79537200	Weak transcription	NHDF-Ad	bronchial

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