Variant report

Variant	rs4608108
Chromosome Location	chr8:48515523-48515524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48513464..48515742-chr8:48650061..48652115,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221869	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10094128	0.82[CEU][hapmap]
rs1038797	0.95[JPT][hapmap]
rs10808752	0.95[JPT][hapmap]
rs10957549	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10957644	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10958058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1106607	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11778548	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11781727	1.00[ASW][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap]
rs11782572	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11784823	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12544329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12549996	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12675378	0.96[EUR][1000 genomes]
rs12678110	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12682269	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs16928696	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1872840	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2129617	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2129618	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2130412	0.97[EUR][1000 genomes]
rs2130413	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4489323	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536257	0.96[CEU][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4594029	0.82[CEU][hapmap]
rs4873102	0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4873368	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4873395	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4873399	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4873437	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4873478	0.82[CEU][hapmap]
rs4873507	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4873529	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4873546	0.81[CEU][hapmap]
rs4873565	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4873619	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55941013	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56092229	0.94[EUR][1000 genomes]
rs62539116	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62539144	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62539147	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62539150	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6982620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6986054	0.82[CEU][hapmap]
rs6987043	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6989917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7014443	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7826284	0.95[JPT][hapmap]
rs7842068	0.82[CEU][hapmap]
rs876915	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs923499	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv890848	chr8:48405007-48535622	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv470211	chr8:48405007-48545961	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1029297	chr8:48468835-48530803	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030163	chr8:48468835-48544495	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4608108	KIAA0146	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48466800-48522600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:48498600-48522600	Weak transcription	Fetal Stomach	stomach
3	chr8:48503600-48535000	Weak transcription	Dnd41	blood
4	chr8:48503800-48515600	Weak transcription	Fetal Intestine Large	intestine
5	chr8:48506400-48522600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr8:48506600-48516800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:48506600-48516800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:48506600-48517000	Weak transcription	Gastric	stomach
9	chr8:48506600-48525400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:48506600-48530600	Weak transcription	HepG2	liver
11	chr8:48507200-48522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:48507800-48522400	Weak transcription	HSMM	muscle
13	chr8:48508400-48517800	Weak transcription	HSMMtube	muscle
14	chr8:48508400-48518400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:48509800-48518600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr8:48510000-48518400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:48510200-48516400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr8:48510200-48516800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr8:48510400-48516400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr8:48510400-48523400	Weak transcription	Hela-S3	cervix
21	chr8:48510600-48517400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr8:48510600-48522800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr8:48510600-48523000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr8:48510600-48545400	Weak transcription	Esophagus	oesophagus
25	chr8:48511600-48517400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr8:48511600-48518400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr8:48511800-48516000	Weak transcription	Right Atrium	heart
28	chr8:48511800-48516800	Weak transcription	Psoas Muscle	Psoas
29	chr8:48511800-48516800	Weak transcription	Right Ventricle	heart
30	chr8:48511800-48519400	Weak transcription	Ovary	ovary
31	chr8:48511800-48521200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:48511800-48523000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr8:48512000-48517800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr8:48512200-48556600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr8:48512400-48516200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr8:48512400-48522800	Weak transcription	Aorta	Aorta
37	chr8:48512400-48522800	Weak transcription	Spleen	Spleen
38	chr8:48513000-48516800	Weak transcription	Primary T cells from cord blood	blood
39	chr8:48513000-48532000	Weak transcription	Fetal Intestine Small	intestine
40	chr8:48513200-48516000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr8:48513600-48516400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr8:48513600-48522800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr8:48513800-48520000	Weak transcription	A549	lung
44	chr8:48514000-48515600	Enhancers	Fetal Muscle Leg	muscle
45	chr8:48514000-48515800	Enhancers	Primary hematopoietic stem cells	blood
46	chr8:48514000-48518000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr8:48514000-48520600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:48514000-48536800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr8:48514200-48516000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr8:48514200-48522200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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