Variant report

Variant	rs6862105
Chromosome Location	chr5:179470642-179470643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179469293..179473403-chr5:179473812..179477504,5	MCF-7	breast:
2	chr5:179461642..179463908-chr5:179470350..179472207,2	K562	blood:
3	chr5:179466042..179468757-chr5:179469985..179473584,3	K562	blood:
4	chr5:179469780..179472209-chr5:179474467..179476576,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10051632	0.82[AFR][1000 genomes]
rs10051694	0.92[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];0.88[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10056316	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10056991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059400	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10066845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071652	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]
rs10079029	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10464058	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11249663	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249666	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739706	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739898	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap]
rs11748441	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11750102	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];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435998	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278662	0.86[JPT][hapmap]
rs34585953	0.80[EUR][1000 genomes]
rs3776946	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776948	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264913	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700852	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]
rs4700854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700859	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4700864	0.83[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs57008562	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57117216	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61356660	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62404970	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62404974	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62404976	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404977	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404979	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405015	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6601078	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884565	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]
rs6898203	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7729516	0.90[EUR][1000 genomes]
rs7734329	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9329095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6862105	GRM6	cis	cerebellum	SCAN
rs6862105	TRIM7	cis	parietal	SCAN
rs6862105	RASGEF1C	cis	cerebellum	SCAN
rs6862105	LTC4S	cis	cerebellum	SCAN
rs6862105	C5orf45	cis	parietal	SCAN
rs6862105	PROP1	cis	parietal	SCAN
rs6862105	CLTB	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179462800-179474800	Weak transcription	Fetal Heart	heart
5	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
6	chr5:179463600-179472800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:179463600-179473400	Weak transcription	HUVEC	blood vessel
8	chr5:179463600-179475600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
10	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:179464400-179473200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:179464400-179473400	Weak transcription	Spleen	Spleen
14	chr5:179464400-179476800	Weak transcription	HepG2	liver
15	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:179464600-179470800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:179464600-179471200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:179464600-179472400	Weak transcription	Placenta	Placenta
19	chr5:179464600-179473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:179464600-179473800	Weak transcription	Right Ventricle	heart
21	chr5:179464600-179474400	Weak transcription	Primary T cells from cord blood	blood
22	chr5:179464800-179473200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:179464800-179473800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:179465200-179472800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:179465200-179473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:179465200-179474800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:179465200-179474800	Weak transcription	Psoas Muscle	Psoas
29	chr5:179465200-179475800	Weak transcription	HSMMtube	muscle
30	chr5:179465400-179471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179465400-179472200	Weak transcription	Fetal Stomach	stomach
32	chr5:179465400-179472400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:179465400-179472800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:179465400-179473200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:179465400-179473400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:179465400-179473400	Weak transcription	Primary B cells from cord blood	blood
37	chr5:179465400-179473600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:179465400-179474600	Weak transcription	Lung	lung
39	chr5:179465400-179477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
41	chr5:179465600-179474800	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:179467200-179471000	Enhancers	Fetal Brain Male	brain
43	chr5:179467200-179472200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:179467400-179473000	Weak transcription	Brain Germinal Matrix	brain
45	chr5:179467400-179474600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:179467400-179474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:179467400-179483200	Weak transcription	HSMM	muscle
48	chr5:179467600-179472800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:179467600-179473000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:179467600-179473600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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