Variant report

Variant	rs576420
Chromosome Location	chr6:143072350-143072351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs578343	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580717	0.84[ASN][1000 genomes]
rs584733	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs597493	0.89[ASN][1000 genomes]
rs630537	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs638880	0.84[ASN][1000 genomes]
rs643298	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs654730	0.87[ASN][1000 genomes]
rs657775	0.89[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs576420	HIVEP2	cis	parietal	SCAN
rs576420	HIVEP2	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143049800-143073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:143054200-143072800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:143059400-143072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:143059400-143080600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:143059600-143074200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:143059800-143072400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:143062200-143074200	Weak transcription	NHEK	skin
8	chr6:143062400-143073600	Weak transcription	NHDF-Ad	bronchial
9	chr6:143062400-143074200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:143062600-143074200	Weak transcription	HSMM	muscle
11	chr6:143064000-143074000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:143066000-143073000	Weak transcription	HSMMtube	muscle
13	chr6:143066200-143074200	Weak transcription	HMEC	breast
14	chr6:143066200-143079000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:143066800-143074000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:143066800-143074200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:143067600-143074200	Weak transcription	Brain Angular Gyrus	brain
18	chr6:143067600-143080600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:143067800-143074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:143067800-143074200	Weak transcription	Aorta	Aorta
21	chr6:143067800-143074200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:143068000-143072800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:143068000-143074200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:143068000-143074200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:143068000-143075000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:143068200-143073800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:143068200-143074200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:143068200-143074200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:143068200-143074200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:143068200-143074200	Weak transcription	Thymus	Thymus
31	chr6:143068200-143077400	Weak transcription	Fetal Lung	lung
32	chr6:143068200-143079600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:143068400-143072800	Weak transcription	Fetal Thymus	thymus
34	chr6:143068400-143074000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:143069400-143072600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:143070600-143073800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:143070600-143074200	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:143071000-143072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:143071000-143073800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:143071200-143072800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:143071200-143072800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:143071200-143072800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:143071200-143072800	Weak transcription	Fetal Intestine Large	intestine
44	chr6:143071200-143072800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:143071200-143074200	Weak transcription	Liver	Liver
46	chr6:143071200-143074200	Weak transcription	HepG2	liver
47	chr6:143071200-143074400	Weak transcription	Fetal Stomach	stomach
48	chr6:143071400-143073000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:143071400-143073000	Weak transcription	Left Ventricle	heart
50	chr6:143071600-143073400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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