Variant report

Variant	rs7823349
Chromosome Location	chr8:10998630-10998631
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10087081	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10105377	0.92[ASN][1000 genomes]
rs10106207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10106914	0.82[CHB][hapmap]
rs10503415	1.00[JPT][hapmap]
rs10503416	0.82[CHB][hapmap]
rs11250117	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs11250119	0.82[JPT][hapmap]
rs11991716	0.85[CEU][hapmap]
rs17724467	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17783634	0.82[CHB][hapmap]
rs2409694	0.88[CEU][hapmap]
rs2409710	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2409712	0.82[CHB][hapmap]
rs2409713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409714	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409715	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409716	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409717	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409718	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2409742	0.82[CHB][hapmap]
rs28417109	0.92[ASN][1000 genomes]
rs28630509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28887839	0.86[EUR][1000 genomes]
rs3021494	0.82[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs3021500	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs34162231	0.84[EUR][1000 genomes]
rs34772085	0.92[ASN][1000 genomes]
rs4333549	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4523214	0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4840544	0.84[ASN][1000 genomes]
rs4840549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840551	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4841495	0.81[ASN][1000 genomes]
rs4841498	0.82[CHB][hapmap]
rs4841500	0.82[CHB][hapmap]
rs4841501	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841503	0.86[ASN][1000 genomes]
rs60921132	0.89[ASN][1000 genomes]
rs6601564	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs67849263	0.83[EUR][1000 genomes]
rs6986002	0.80[EUR][1000 genomes]
rs6986032	0.82[CHB][hapmap]
rs6995204	0.86[ASN][1000 genomes]
rs6996752	0.88[CHD][hapmap]
rs6996846	0.92[ASN][1000 genomes]
rs7004825	0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7005680	0.82[ASN][1000 genomes]
rs7010590	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7011756	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs7460507	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7813802	0.82[CHB][hapmap]
rs7829396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1019796	chr8:10979442-11010826	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7823349	TDH	cis	cerebellum	SCAN
rs7823349	DEFB134	cis	cerebellum	SCAN
rs7823349	MFHAS1	cis	cerebellum	SCAN
rs7823349	FLJ10661	cis	cerebellum	SCAN
rs7823349	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs7823349	CTSB	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:10982800-11003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr8:10983000-11002000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:10983000-11003200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr8:10983200-11001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:10984400-11000000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr8:10986400-11002000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:10989600-11014200	Weak transcription	Pancreas	Pancrea
10	chr8:10991800-10998800	Weak transcription	Gastric	stomach
11	chr8:10991800-11011800	Weak transcription	Left Ventricle	heart
12	chr8:10992800-11002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:10995600-10999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr8:10997000-11001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:10997000-11002000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr8:10997200-10999000	Weak transcription	Esophagus	oesophagus
17	chr8:10997200-11021000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:10997400-10998800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:10997400-10999000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:10997400-10999000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:10997400-10999000	Weak transcription	Spleen	Spleen
22	chr8:10997400-11001800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr8:10997400-11002000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:10997400-11003800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:10997400-11006000	Weak transcription	HSMMtube	muscle
26	chr8:10997400-11011200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr8:10997400-11017400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr8:10997600-10999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr8:10997600-11002000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr8:10998000-11001800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr8:10998000-11002000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr8:10998200-11002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:10998600-10998800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:10998600-11002000	Weak transcription	Primary hematopoietic stem cells	blood

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