Variant report

Variant	rs847845
Chromosome Location	chr6:34923864-34923865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10807143	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10947533	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947534	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10947535	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10947536	0.82[MEX][hapmap]
rs11755713	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13215944	0.81[ASN][1000 genomes]
rs16895035	0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs16895354	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1737724	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1883639	0.81[ASN][1000 genomes]
rs2030611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2140418	0.94[ASW][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap]
rs2177381	0.82[MEX][hapmap]
rs2293242	0.82[MEX][hapmap]
rs2395601	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34006431	0.81[ASN][1000 genomes]
rs35057781	0.82[ASN][1000 genomes]
rs35499928	0.81[ASN][1000 genomes]
rs35760768	0.81[ASN][1000 genomes]
rs35786848	0.81[ASN][1000 genomes]
rs3734258	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3734259	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3756859	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777750	0.88[JPT][hapmap]
rs3800443	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3800448	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3800450	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3800452	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3800453	0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3822923	0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4646920	0.80[ASN][1000 genomes]
rs56140217	0.97[ASN][1000 genomes]
rs56248791	0.80[ASN][1000 genomes]
rs57955553	0.81[ASN][1000 genomes]
rs6457799	0.94[ASW][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs6907427	0.81[ASN][1000 genomes]
rs6912229	0.86[ASN][1000 genomes]
rs6913108	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6918498	0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6927009	0.81[ASN][1000 genomes]
rs6941065	0.82[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs73745049	0.82[ASN][1000 genomes]
rs73745050	0.82[ASN][1000 genomes]
rs7740148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7751820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7752468	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7755801	0.81[ASN][1000 genomes]
rs7756122	0.81[ASN][1000 genomes]
rs847842	0.91[ASN][1000 genomes]
rs847844	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs847848	0.82[MEX][hapmap]
rs847861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847862	0.93[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs861878	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9357187	0.80[ASN][1000 genomes]
rs9368835	0.80[ASN][1000 genomes]
rs9368837	0.80[ASN][1000 genomes]
rs9380465	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380466	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380467	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9380468	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9380470	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9380476	0.93[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9380481	0.81[ASN][1000 genomes]
rs9394254	0.81[ASN][1000 genomes]
rs9394255	0.81[ASN][1000 genomes]
rs9784889	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Non-small cell lung cancer	23144319	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs847845	C6orf129	cis	parietal	SCAN
rs847845	TAF11	cis	cerebellum	SCAN
rs847845	ANKS1A	cis	normal skin	skin_eQTL
rs847845	TAF11	cis	parietal	SCAN
rs847845	PRDM7	trans	multi-tissue	Pritchard
rs847845	SLC26A8	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34881200-34928200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:34895800-34949200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:34896000-34934600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:34903200-34927800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:34904600-34937400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:34907400-34937600	Weak transcription	Dnd41	blood
7	chr6:34912400-34928000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:34915800-34926600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:34916800-34927800	Weak transcription	Lung	lung
10	chr6:34917200-34926800	Weak transcription	Spleen	Spleen
11	chr6:34918600-34938400	Weak transcription	Thymus	Thymus
12	chr6:34918800-34924400	Weak transcription	Psoas Muscle	Psoas
13	chr6:34919000-34929600	Weak transcription	Fetal Kidney	kidney
14	chr6:34919600-34926400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr6:34919800-34937200	Weak transcription	NHEK	skin
16	chr6:34920000-34925800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:34920000-34937400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:34920000-34937400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:34920400-34958600	Weak transcription	Colonic Mucosa	Colon
20	chr6:34920800-34925400	Weak transcription	Small Intestine	intestine
21	chr6:34921000-34925800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:34921200-34925600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:34921200-34925800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:34921200-34937600	Weak transcription	Aorta	Aorta
25	chr6:34921200-34949400	Weak transcription	Esophagus	oesophagus
26	chr6:34921400-34924600	Weak transcription	Fetal Lung	lung
27	chr6:34921400-34925800	Weak transcription	Placenta	Placenta
28	chr6:34921400-34927800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:34921400-34937400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:34921600-34924400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:34921600-34924400	Weak transcription	Left Ventricle	heart
32	chr6:34921600-34924400	Weak transcription	Right Ventricle	heart
33	chr6:34921600-34926800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:34921600-34937600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:34921600-34937800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:34921600-34949400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:34921800-34924400	Weak transcription	Brain Anterior Caudate	brain
38	chr6:34921800-34938800	Weak transcription	HMEC	breast
39	chr6:34922000-34925000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:34922000-34928200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:34922000-34953800	Weak transcription	Hela-S3	cervix
42	chr6:34922200-34924400	Weak transcription	Fetal Heart	heart
43	chr6:34922200-34924600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:34922200-34924600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:34922200-34924600	Weak transcription	Brain Substantia Nigra	brain
46	chr6:34922200-34925000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:34922200-34932200	Weak transcription	Osteobl	bone
48	chr6:34922200-34937400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:34922400-34924600	Weak transcription	Liver	Liver
50	chr6:34922400-34924800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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