Variant report

Variant	rs6872396
Chromosome Location	chr5:75823965-75823966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12522582	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4145111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704320	1.00[JPT][hapmap]
rs4704323	1.00[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4704324	0.87[CEU][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6453230	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS 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	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6872396	GFM2	cis	parietal	SCAN
rs6872396	ARSB	cis	cerebellum	SCAN
rs6872396	TMEM171	cis	parietal	SCAN
rs6872396	POC5	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75806800-75834200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:75806800-75839200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:75810600-75828400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:75815000-75829000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:75815200-75828000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:75816400-75826800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:75817800-75827800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:75818200-75824000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:75818200-75828400	Weak transcription	Gastric	stomach
10	chr5:75818400-75830800	Weak transcription	Pancreas	Pancrea
11	chr5:75819200-75824200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:75819400-75828200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:75820000-75826200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr5:75820200-75827600	Enhancers	Primary hematopoietic stem cells	blood
15	chr5:75820200-75832600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:75820600-75825600	Weak transcription	Liver	Liver
17	chr5:75821000-75824200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:75821000-75824800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr5:75821000-75826800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:75821200-75828400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:75821600-75825000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr5:75821800-75828400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:75822000-75824200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr5:75822200-75824000	Enhancers	Fetal Stomach	stomach
25	chr5:75822200-75831200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:75822200-75831200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:75822800-75824000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:75822800-75824200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:75822800-75825000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr5:75823000-75824000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:75823000-75825200	Enhancers	K562	blood
32	chr5:75823000-75838400	Weak transcription	Primary T cells from cord blood	blood
33	chr5:75823200-75824000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:75823200-75824000	Weak transcription	Fetal Thymus	thymus
35	chr5:75823200-75824400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:75823200-75824800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr5:75823200-75825000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr5:75823200-75830000	Weak transcription	Stomach Mucosa	stomach
39	chr5:75823200-75830800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:75823400-75824000	Enhancers	HMEC	breast
41	chr5:75823400-75824000	Enhancers	NHEK	skin
42	chr5:75823400-75824200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:75823400-75824200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:75823400-75824400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:75823400-75824600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:75823400-75824600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:75823400-75828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:75823400-75828400	Weak transcription	Lung	lung
49	chr5:75823400-75832000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr5:75823600-75824000	Enhancers	H9 Cell Line	embryonic stem cell

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