Variant report

Variant	rs6605610
Chromosome Location	chr8:86160851-86160852
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	chr8:86131617..86133252-chr8:86160556..86162129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176731	Chromatin interaction
ENSG00000185015	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10088120	0.95[JPT][hapmap]
rs10090196	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10091582	0.83[ASN][1000 genomes]
rs10099251	0.83[ASN][1000 genomes]
rs10100442	0.89[JPT][hapmap]
rs10106970	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10110461	0.82[ASN][1000 genomes]
rs10111971	0.83[ASN][1000 genomes]
rs1021583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11261468	0.85[JPT][hapmap]
rs11261469	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11261471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11261474	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11985733	0.82[JPT][hapmap]
rs12541299	0.84[ASN][1000 genomes]
rs12541445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12543256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12544332	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12546106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12679400	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1303806	0.87[JPT][hapmap]
rs13252971	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13259399	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs13259464	0.92[ASN][1000 genomes]
rs13269739	0.95[JPT][hapmap]
rs1390711	0.87[JPT][hapmap]
rs1493302	0.83[JPT][hapmap]
rs1496529	0.83[JPT][hapmap]
rs1496530	0.82[JPT][hapmap]
rs1496531	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496532	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1532424	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1553015	0.86[JPT][hapmap]
rs1553016	0.83[ASN][1000 genomes]
rs1553017	0.82[ASN][1000 genomes]
rs16913681	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16913721	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17740658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1845891	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1845892	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1908762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995056	0.81[JPT][hapmap]
rs1995057	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1995058	0.86[JPT][hapmap]
rs2006767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs20571	0.82[JPT][hapmap]
rs2072696	0.82[JPT][hapmap]
rs2132589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2132590	0.90[ASN][1000 genomes]
rs2278459	0.85[JPT][hapmap]
rs2279700	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2279701	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291787	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2403083	0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2403084	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2403085	0.92[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2403086	0.92[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2403088	0.85[JPT][hapmap]
rs2403104	0.86[JPT][hapmap]
rs28374336	0.83[ASN][1000 genomes]
rs28377260	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28439950	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28564613	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28677919	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2896452	0.85[JPT][hapmap]
rs2896454	0.95[JPT][hapmap]
rs34103685	0.95[JPT][hapmap]
rs35558766	0.82[ASN][1000 genomes]
rs3779899	0.95[JPT][hapmap]
rs3779901	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3808538	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs3808539	0.86[JPT][hapmap]
rs4150867	0.95[JPT][hapmap]
rs4150868	0.95[JPT][hapmap]
rs4150869	0.90[JPT][hapmap]
rs4150893	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs4150897	0.84[ASN][1000 genomes]
rs4150909	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4150942	0.85[JPT][hapmap]
rs4150944	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4150962	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4150964	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4150974	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4150977	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4609189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4617148	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4739698	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4739700	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4740043	0.81[JPT][hapmap]
rs4740044	0.91[JPT][hapmap]
rs4740045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4740047	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4740049	0.86[JPT][hapmap]
rs6605611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6605613	0.82[ASN][1000 genomes]
rs6605624	0.85[JPT][hapmap]
rs6990449	0.93[JPT][hapmap]
rs6993316	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6993387	0.91[JPT][hapmap]
rs6994113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7001359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7004871	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7008772	0.91[JPT][hapmap]
rs7011001	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7011926	0.86[JPT][hapmap]
rs7015758	0.95[JPT][hapmap]
rs7818163	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7821629	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7826589	0.81[JPT][hapmap]
rs7827175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7829050	0.95[JPT][hapmap]
rs7829144	0.85[JPT][hapmap]
rs7829240	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7839129	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7841142	0.85[JPT][hapmap]
rs903895	0.86[JPT][hapmap]
rs903896	0.86[JPT][hapmap]
rs903897	0.87[JPT][hapmap]
rs9329908	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9987281	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv971329	chr8:86094967-86183119	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2761441	chr8:86155592-86167129	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6605610	LRRCC1	cis	normal skin	skin_eQTL
rs6605610	CA13	cis	multi-tissue	Pritchard
rs6605610	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs6605610	CA13	cis	Lymphoblastoid	GTEx
rs6605610	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs6605610	LRRCC1	cis	Esophagus Mucosa	GTEx
rs6605610	LRRCC1	cis	Artery Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86158400-86172600	Weak transcription	Left Ventricle	heart
2	chr8:86158400-86174000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr8:86158400-86178200	Weak transcription	Small Intestine	intestine
4	chr8:86158400-86178200	Weak transcription	Stomach Mucosa	stomach
5	chr8:86158400-86179400	Weak transcription	Gastric	stomach
6	chr8:86158400-86180800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr8:86158400-86185800	Weak transcription	Lung	lung
8	chr8:86158400-86188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:86158400-86188200	Weak transcription	Esophagus	oesophagus
10	chr8:86158400-86191400	Weak transcription	Pancreas	Pancrea
11	chr8:86158800-86162000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr8:86158800-86163200	Weak transcription	Fetal Intestine Small	intestine
13	chr8:86158800-86167000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr8:86158800-86167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:86158800-86171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr8:86158800-86171200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr8:86158800-86172400	Weak transcription	Fetal Intestine Large	intestine
18	chr8:86158800-86179400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr8:86158800-86185600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr8:86158800-86185800	Weak transcription	Fetal Stomach	stomach
21	chr8:86158800-86186800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:86158800-86189600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:86158800-86191400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr8:86159000-86166600	Weak transcription	NHEK	skin
25	chr8:86159000-86171200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr8:86159600-86167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:86160000-86169200	Weak transcription	Fetal Lung	lung
28	chr8:86160000-86172600	Weak transcription	HepG2	liver

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