Variant report

Variant	rs7642430
Chromosome Location	chr3:143257069-143257070
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	chr3:143256524..143258792-chr3:143259054..143261566,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11922426	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12494880	0.80[TSI][hapmap]
rs13061398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13064748	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs13068070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13069703	0.90[EUR][1000 genomes]
rs13071089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074737	0.86[TSI][hapmap]
rs13076949	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs13085205	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13090915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1405017	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1525858	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1525862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1525863	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs16853857	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs17640925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1983467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289451	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35417581	0.90[EUR][1000 genomes]
rs35593863	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839601	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4839602	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs4839642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59016370	0.92[AFR][1000 genomes]
rs71307941	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71307942	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72999717	0.88[AFR][1000 genomes]
rs72999725	0.92[AFR][1000 genomes]
rs72999726	0.92[AFR][1000 genomes]
rs72999743	0.92[AFR][1000 genomes]
rs72999747	0.87[AFR][1000 genomes]
rs746055	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[TSI][hapmap];0.90[EUR][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7642430	TFDP2	cis	cerebellum	SCAN
rs7642430	GK5	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143248400-143261000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr3:143248400-143263800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:143248400-143276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:143250200-143269600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:143252200-143269400	Weak transcription	Placenta	Placenta
6	chr3:143254800-143257600	Enhancers	Dnd41	blood
7	chr3:143254800-143258400	Enhancers	NHLF	lung
8	chr3:143255000-143258400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:143255000-143258400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:143255000-143258400	Enhancers	Fetal Stomach	stomach
11	chr3:143255200-143257400	Weak transcription	Colonic Mucosa	Colon
12	chr3:143255200-143257600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:143255200-143257600	Weak transcription	Fetal Kidney	kidney
14	chr3:143255400-143257400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:143255400-143258000	Enhancers	HSMM	muscle
16	chr3:143255600-143257200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:143255600-143257400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:143255600-143257400	Enhancers	NHDF-Ad	bronchial
19	chr3:143255600-143258400	Enhancers	Adipose Nuclei	Adipose
20	chr3:143255600-143276800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:143255800-143267200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:143255800-143271800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:143256000-143257200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:143256000-143258200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:143256000-143258200	Enhancers	GM12878-XiMat	blood
26	chr3:143256000-143258400	Enhancers	Osteobl	bone
27	chr3:143256000-143305600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:143256200-143257200	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:143256200-143268000	Weak transcription	Brain Substantia Nigra	brain
30	chr3:143256400-143257200	Weak transcription	HSMMtube	muscle
31	chr3:143256400-143257400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:143256400-143257400	Weak transcription	Small Intestine	intestine
33	chr3:143256400-143257400	Weak transcription	HMEC	breast
34	chr3:143256400-143258600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:143256400-143266800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:143256400-143270000	Weak transcription	Spleen	Spleen
37	chr3:143256600-143264400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:143256600-143275000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:143256800-143258400	Enhancers	Fetal Lung	lung
40	chr3:143256800-143269400	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:143256800-143269800	Weak transcription	Esophagus	oesophagus
42	chr3:143256800-143277000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:143257000-143257400	Weak transcription	Ovary	ovary
44	chr3:143257000-143258200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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