Variant report

Variant	rs9470825
Chromosome Location	chr6:38162310-38162311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38147181..38149521-chr6:38161439..38163786,2	K562	blood:
2	chr6:38116607..38119118-chr6:38160290..38163067,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10807190	0.80[CEU][hapmap];0.80[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10807191	0.89[CHD][hapmap];0.83[GIH][hapmap];0.91[ASN][1000 genomes]
rs10807192	0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs10947714	1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10947716	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11754110	0.89[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs11756830	0.89[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs12196879	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12197001	0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs12198616	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs12206712	0.83[CHD][hapmap]
rs13205068	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs13212638	0.89[CHD][hapmap];0.90[GIH][hapmap]
rs17678747	0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs17678833	0.84[ASN][1000 genomes]
rs2143403	0.82[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs2235710	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2235711	0.87[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3800358	0.83[CHD][hapmap]
rs3823431	0.92[ASN][1000 genomes]
rs4314486	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4510661	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs6458044	0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6938410	0.95[ASN][1000 genomes]
rs735117	0.83[CHD][hapmap]
rs737171	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742537	0.88[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs742538	0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs761153	0.87[EUR][1000 genomes]
rs7742915	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756835	0.82[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs909998	0.83[CHD][hapmap]
rs926565	0.84[ASN][1000 genomes]
rs9380721	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462400	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9462404	0.86[CEU][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9462405	0.84[ASN][1000 genomes]
rs9462406	0.88[ASN][1000 genomes]
rs9462409	0.84[ASN][1000 genomes]
rs9470806	0.87[EUR][1000 genomes]
rs9470807	0.89[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9470811	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470813	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9470816	0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470818	0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470819	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470820	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470822	0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470823	0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470824	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9470825	ZFAND3	cis	cerebellum	SCAN
rs9470825	TRERF1	cis	cerebellum	SCAN
rs9470825	GLO1	cis	parietal	SCAN
rs9470825	C6orf64	cis	cerebellum	SCAN
rs9470825	TMEM217	cis	parietal	SCAN
rs9470825	C6orf126	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
3	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:38141600-38166200	Weak transcription	Left Ventricle	heart
6	chr6:38141800-38168000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38143600-38162400	Weak transcription	Right Ventricle	heart
8	chr6:38143600-38177200	Weak transcription	Ovary	ovary
9	chr6:38145200-38163400	Weak transcription	Colonic Mucosa	Colon
10	chr6:38146000-38162400	Weak transcription	Pancreas	Pancrea
11	chr6:38146400-38162400	Weak transcription	Gastric	stomach
12	chr6:38146600-38162400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:38147400-38180400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:38152000-38166600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:38153800-38164400	Weak transcription	Primary B cells from cord blood	blood
16	chr6:38155600-38177200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:38155800-38162800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:38156000-38162400	Weak transcription	Aorta	Aorta
19	chr6:38156000-38162800	Weak transcription	Brain Substantia Nigra	brain
20	chr6:38157800-38166200	Weak transcription	Psoas Muscle	Psoas
21	chr6:38158200-38163200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:38158800-38162400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:38159200-38162600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:38159200-38162600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:38159600-38162800	Strong transcription	Primary T cells from cord blood	blood
26	chr6:38160000-38164000	Weak transcription	Fetal Intestine Small	intestine
27	chr6:38160000-38166000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:38160200-38177600	Weak transcription	Esophagus	oesophagus
29	chr6:38160400-38177000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:38160400-38177600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:38160600-38162600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:38160600-38165000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:38160600-38177000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:38160600-38179600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:38161000-38162600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:38161000-38162600	Enhancers	Brain Anterior Caudate	brain
38	chr6:38161000-38162600	Enhancers	Lung	lung
39	chr6:38161000-38162800	Enhancers	Fetal Muscle Trunk	muscle
40	chr6:38161000-38163200	Enhancers	Brain Germinal Matrix	brain
41	chr6:38161200-38162600	Enhancers	Fetal Muscle Leg	muscle
42	chr6:38161200-38167400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:38161400-38162400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:38161600-38162600	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:38161600-38162600	Weak transcription	Fetal Brain Female	brain
46	chr6:38161600-38162600	Enhancers	HSMM	muscle
47	chr6:38161600-38163000	Enhancers	Fetal Stomach	stomach
48	chr6:38161600-38175200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:38162000-38162600	Enhancers	Spleen	Spleen
50	chr6:38162000-38179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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