Variant report

Variant	rs2398132
Chromosome Location	chr6:100981200-100981201
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10457808	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782302	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs108422	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11155496	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155498	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12190903	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191199	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192249	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12200565	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12206182	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12206564	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12206945	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12374612	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12660725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151573	0.80[EUR][1000 genomes]
rs17303769	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875400	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875401	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2001102	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062634	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062635	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239237	0.80[EUR][1000 genomes]
rs239238	0.80[EUR][1000 genomes]
rs239239	0.80[EUR][1000 genomes]
rs239242	0.80[EUR][1000 genomes]
rs239245	0.80[EUR][1000 genomes]
rs239246	0.80[EUR][1000 genomes]
rs239247	0.80[EUR][1000 genomes]
rs239249	0.80[EUR][1000 genomes]
rs240110	0.83[ASN][1000 genomes]
rs240112	0.83[ASN][1000 genomes]
rs240115	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs240143	0.80[EUR][1000 genomes]
rs240145	0.80[EUR][1000 genomes]
rs240146	0.80[EUR][1000 genomes]
rs240153	0.81[ASN][1000 genomes]
rs240154	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240156	0.83[ASN][1000 genomes]
rs240164	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs240764	0.88[EUR][1000 genomes]
rs395521	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4461738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62422675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv886444	chr6:100961198-101084946	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv969431	chr6:100979137-100981528	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
6	nsv604263	chr6:100980874-101078718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2398132	ASCC3	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100952800-100997400	Weak transcription	A549	lung
2	chr6:100954600-100986200	Weak transcription	Spleen	Spleen
3	chr6:100955800-100991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:100957400-100992400	Weak transcription	Small Intestine	intestine
5	chr6:100960600-100990200	Weak transcription	Brain Substantia Nigra	brain
6	chr6:100960800-100986000	Weak transcription	GM12878-XiMat	blood
7	chr6:100960800-100986200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:100960800-100986600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:100960800-100989600	Weak transcription	K562	blood
10	chr6:100960800-100989800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:100960800-101035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:100961000-100986600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:100961000-100987200	Weak transcription	Osteobl	bone
14	chr6:100961000-100988800	Weak transcription	NHEK	skin
15	chr6:100961000-100991200	Weak transcription	HSMMtube	muscle
16	chr6:100961000-100992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:100961000-100997200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:100961200-100989000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:100961400-100986000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:100963000-100986800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:100964000-100990800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:100964200-100986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:100964200-101020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:100964800-100998400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:100965200-100984000	Weak transcription	HepG2	liver
26	chr6:100965200-100986600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:100965200-100989600	Weak transcription	Aorta	Aorta
28	chr6:100965200-100990200	Weak transcription	Left Ventricle	heart
29	chr6:100965200-101000800	Weak transcription	Fetal Intestine Small	intestine
30	chr6:100965200-101011400	Weak transcription	Pancreas	Pancrea
31	chr6:100965400-100984200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:100965400-100984400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:100965400-100984400	Weak transcription	Psoas Muscle	Psoas
34	chr6:100965400-100985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:100965400-100986600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:100965400-100988600	Weak transcription	Lung	lung
37	chr6:100965400-100989600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:100965400-100989800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:100965400-100990400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:100965400-100991800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:100965400-101005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:100965600-100986800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:100965600-100987000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:100965600-100987800	Weak transcription	Adipose Nuclei	Adipose
45	chr6:100965600-101033600	Weak transcription	Ovary	ovary
46	chr6:100965800-100984400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:100965800-100987400	Weak transcription	Placenta	Placenta
48	chr6:100966000-101002400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:100966200-100983000	Weak transcription	Dnd41	blood
50	chr6:100966200-100984400	Weak transcription	Primary T cells fromperipheralblood	blood

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