Variant report

Variant	rs6605624
Chromosome Location	chr8:86042814-86042815
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86041361..86043204-chr8:86048252..86049988,2	MCF-7	breast:
2	chr8:86041424..86043525-chr8:86089868..86091412,2	MCF-7	breast:
3	chr8:86018609..86020657-chr8:86041368..86044315,2	K562	blood:

Variant related genes	Relation type
ENSG00000254208	Chromatin interaction
ENSG00000133739	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10088120	0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10090196	0.95[JPT][hapmap]
rs10091577	0.80[EUR][1000 genomes]
rs10091710	0.81[EUR][1000 genomes]
rs10100442	0.84[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10104630	0.81[JPT][hapmap]
rs1021583	0.85[JPT][hapmap]
rs11261468	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11261471	0.80[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs12541445	0.80[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs12543256	0.85[JPT][hapmap]
rs12546106	0.85[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs12550160	0.85[JPT][hapmap]
rs13249364	0.81[EUR][1000 genomes]
rs13259399	0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs13269031	0.82[EUR][1000 genomes]
rs13269739	0.90[JPT][hapmap]
rs1390711	0.90[JPT][hapmap]
rs1553015	0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs16913681	0.85[JPT][hapmap]
rs16913721	0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs17740658	0.85[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1908762	0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2006767	0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs2132589	0.85[JPT][hapmap]
rs2278459	0.87[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2279701	0.80[JPT][hapmap]
rs2291786	0.85[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs2291787	0.80[JPT][hapmap]
rs2403082	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2403083	0.90[JPT][hapmap]
rs2403085	0.90[JPT][hapmap]
rs2403086	0.90[JPT][hapmap]
rs2403087	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403088	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403089	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2403104	0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2896452	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2896453	0.87[AMR][1000 genomes]
rs2896454	0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs34103685	0.90[JPT][hapmap];0.84[MEX][hapmap]
rs3779899	0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs3779901	0.85[JPT][hapmap]
rs3808538	1.00[ASW][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes]
rs3808539	0.90[JPT][hapmap]
rs4150862	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150865	0.83[EUR][1000 genomes]
rs4150867	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs4150868	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs4150869	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs4150884	0.81[EUR][1000 genomes]
rs4150893	0.90[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs4150909	0.90[JPT][hapmap]
rs4150942	0.87[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs4150944	0.90[JPT][hapmap]
rs4150964	0.85[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4150974	0.85[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4150977	0.85[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4609189	0.85[JPT][hapmap]
rs4739700	0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs4740043	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740044	0.95[JPT][hapmap];0.90[YRI][hapmap]
rs4740045	0.85[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs62527168	0.81[EUR][1000 genomes]
rs62527173	0.81[EUR][1000 genomes]
rs6605609	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6605610	0.85[JPT][hapmap]
rs6605611	0.84[JPT][hapmap]
rs6605625	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67573812	0.81[AMR][1000 genomes]
rs6986704	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6990256	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6990449	0.93[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs6990452	0.82[AMR][1000 genomes]
rs6993387	0.95[JPT][hapmap];0.90[YRI][hapmap]
rs6994113	0.85[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs7001359	0.80[JPT][hapmap]
rs7004765	0.82[EUR][1000 genomes]
rs7007304	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7008772	0.95[JPT][hapmap]
rs7015758	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs72682904	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7814435	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7818090	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7818163	0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs7823218	0.81[EUR][1000 genomes]
rs7826589	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7827175	0.85[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs7829050	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7829144	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7838900	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7841142	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7842013	0.81[EUR][1000 genomes]
rs903895	0.90[JPT][hapmap]
rs903896	0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs903897	0.90[JPT][hapmap]
rs9692962	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1797206	chr8:86023237-86060072	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv1800945	chr8:86030101-86060072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6605624	C8orf59	cis	parietal	SCAN
rs6605624	LRRCC1	cis	Esophagus Mucosa	GTEx
rs6605624	LRRCC1	cis	cerebellum	SCAN
rs6605624	C8orf59	cis	cerebellum	SCAN
rs6605624	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs6605624	LRRCC1	cis	parietal	SCAN
rs6605624	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020000-86057400	Weak transcription	Small Intestine	intestine
2	chr8:86020400-86043800	Weak transcription	NH-A	brain
3	chr8:86020400-86044400	Weak transcription	Fetal Muscle Leg	muscle
4	chr8:86020400-86048400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:86020400-86048400	Weak transcription	Fetal Stomach	stomach
6	chr8:86020400-86049000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr8:86020400-86054800	Weak transcription	Lung	lung
8	chr8:86020400-86055400	Weak transcription	Fetal Kidney	kidney
9	chr8:86020400-86055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:86020400-86056400	Weak transcription	Gastric	stomach
11	chr8:86020400-86057400	Weak transcription	Aorta	Aorta
12	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
13	chr8:86020600-86044200	Weak transcription	Primary T cells from cord blood	blood
14	chr8:86020600-86045800	Weak transcription	Thymus	Thymus
15	chr8:86020600-86048800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr8:86020600-86049000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr8:86020600-86049200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:86020600-86052400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr8:86020600-86054600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr8:86020800-86050600	Weak transcription	Brain Angular Gyrus	brain
22	chr8:86021000-86046000	Weak transcription	Colon Smooth Muscle	Colon
23	chr8:86021000-86049800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr8:86021200-86053600	Weak transcription	Brain Substantia Nigra	brain
25	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
27	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
28	chr8:86021600-86049800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr8:86021800-86045200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:86025200-86057400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr8:86028400-86059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr8:86028600-86056400	Weak transcription	Ovary	ovary
33	chr8:86032400-86045800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr8:86032600-86050400	Weak transcription	HMEC	breast
35	chr8:86032800-86057400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:86033000-86059800	Weak transcription	Fetal Thymus	thymus
37	chr8:86033600-86046000	Weak transcription	Colonic Mucosa	Colon
38	chr8:86033600-86049000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr8:86034600-86051200	Weak transcription	Liver	Liver
40	chr8:86035200-86043600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr8:86035200-86049000	Weak transcription	GM12878-XiMat	blood
42	chr8:86035200-86055600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:86035400-86045600	Weak transcription	Fetal Lung	lung
44	chr8:86036200-86049400	Weak transcription	HSMM	muscle
45	chr8:86036600-86050600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr8:86036800-86050400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
48	chr8:86037400-86056000	Weak transcription	Right Ventricle	heart
49	chr8:86037600-86046400	Strong transcription	Dnd41	blood
50	chr8:86038000-86057200	Weak transcription	Brain Inferior Temporal Lobe	brain

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