Variant report

Variant	rs10498723
Chromosome Location	chr6:25392345-25392346
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: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10498724	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];1.00[ASN][1000 genomes]
rs10946767	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946768	0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12524380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525031	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs12529416	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16890520	0.82[YRI][hapmap]
rs16890531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890562	0.82[CHB][hapmap]
rs2149226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2149228	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];1.00[ASN][1000 genomes]
rs2149229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328882	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];1.00[ASN][1000 genomes]
rs4711083	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712924	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4712925	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4712926	0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712927	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712928	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs4712930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712931	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs55672111	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56248376	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830734	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830739	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72830741	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830745	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830747	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830754	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72830758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769124	0.82[YRI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10498723	LRRC16A	cis	cerebellum	SCAN
rs10498723	HIST1H2BE	cis	parietal	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	chr6:25388200-25392800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:25388400-25392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:25388400-25395800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:25388400-25396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:25388400-25396000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:25389200-25392800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:25389400-25397400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
13	chr6:25389800-25392600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:25390200-25392800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:25390200-25397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:25390200-25399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:25390200-25401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
19	chr6:25390400-25392600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:25390400-25392600	Weak transcription	NHEK	skin
21	chr6:25390400-25394200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:25390400-25401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:25390400-25401600	Weak transcription	HMEC	breast
24	chr6:25390800-25393000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:25390800-25397400	Weak transcription	Aorta	Aorta
26	chr6:25390800-25399200	Weak transcription	Fetal Thymus	thymus
27	chr6:25391000-25392600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:25391000-25392600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:25392000-25393400	Enhancers	Fetal Lung	lung
31	chr6:25392000-25398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:25392200-25392400	Enhancers	Fetal Brain Male	brain
33	chr6:25392200-25393000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:25392200-25393400	Enhancers	NHDF-Ad	bronchial

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