Variant report

Variant	rs716796
Chromosome Location	chr6:25393146-25393147
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	chr6:25387523..25389408-chr6:25391733..25393654,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10456322	1.00[JPT][hapmap]
rs10456323	1.00[JPT][hapmap]
rs10946770	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs11752017	1.00[JPT][hapmap]
rs11759560	1.00[JPT][hapmap]
rs11759648	1.00[JPT][hapmap]
rs12192331	1.00[JPT][hapmap]
rs12192342	1.00[JPT][hapmap]
rs12201737	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12203031	0.94[GIH][hapmap];1.00[JPT][hapmap]
rs12203442	1.00[JPT][hapmap]
rs12207791	1.00[JPT][hapmap]
rs12211739	0.94[GIH][hapmap];1.00[JPT][hapmap]
rs1410443	1.00[JPT][hapmap]
rs150533	1.00[JPT][hapmap]
rs184202	1.00[JPT][hapmap]
rs212927	1.00[JPT][hapmap]
rs212929	1.00[JPT][hapmap]
rs212931	1.00[JPT][hapmap]
rs212932	1.00[JPT][hapmap]
rs212935	1.00[JPT][hapmap]
rs212937	1.00[JPT][hapmap]
rs212939	1.00[JPT][hapmap]
rs212940	1.00[JPT][hapmap]
rs301377	1.00[JPT][hapmap]
rs441472	1.00[JPT][hapmap]
rs453181	1.00[JPT][hapmap]
rs485567	1.00[JPT][hapmap]
rs6902158	1.00[JPT][hapmap]
rs6927384	1.00[JPT][hapmap]
rs6931843	1.00[JPT][hapmap]
rs716798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs760865	1.00[JPT][hapmap]
rs7742338	1.00[JPT][hapmap]
rs7752524	1.00[JPT][hapmap]
rs7762537	1.00[JPT][hapmap]
rs7764258	1.00[JPT][hapmap]
rs880225	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9348685	1.00[JPT][hapmap]
rs9461151	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9461152	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461153	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9467496	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs9467501	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs716796	LRRC16	Cis_1M	lymphoblastoid	RTeQTL
rs716796	ZSCAN12	cis	cerebellum	SCAN
rs716796	LRRC16	cis	multi-tissue	Pritchard
rs716796	OR2B6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25377800-25395600	Weak transcription	Pancreas	Pancrea
3	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
4	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:25388400-25395800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25388400-25396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:25388400-25396000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:25389400-25397400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
10	chr6:25390200-25397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:25390200-25399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:25390200-25401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
14	chr6:25390400-25394200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:25390400-25401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:25390400-25401600	Weak transcription	HMEC	breast
17	chr6:25390800-25397400	Weak transcription	Aorta	Aorta
18	chr6:25390800-25399200	Weak transcription	Fetal Thymus	thymus
19	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:25392000-25393400	Enhancers	Fetal Lung	lung
21	chr6:25392000-25398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:25392200-25393400	Enhancers	NHDF-Ad	bronchial
23	chr6:25392400-25393200	Weak transcription	Fetal Brain Male	brain
24	chr6:25392600-25393400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:25392600-25393400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:25392600-25393400	Enhancers	NHEK	skin
27	chr6:25392600-25393600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:25392800-25393200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:25392800-25393400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:25392800-25393400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:25392800-25393400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:25392800-25394400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr6:25393000-25393400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:25393000-25397200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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