Variant report

Variant	rs6471857
Chromosome Location	chr8:61176951-61176952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61175226..61177364-chr8:61192482..61194475,2	MCF-7	breast:
2	chr8:61171205..61174050-chr8:61175161..61177205,2	K562	blood:

Variant related genes	Relation type
ENSG00000178538	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10086200	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10086341	0.87[AFR][1000 genomes]
rs10086352	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10086449	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10093008	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10094224	0.81[CEU][hapmap]
rs10094523	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10097537	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101374	0.86[AFR][1000 genomes]
rs10109265	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109487	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10435600	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10957125	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11774698	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11774872	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778498	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11781514	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11994317	0.91[AFR][1000 genomes]
rs13266513	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13267008	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13269899	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13269948	0.91[AFR][1000 genomes]
rs13272076	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs13274525	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13280153	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13281067	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1904780	0.81[AFR][1000 genomes]
rs28371059	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28376554	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28429093	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28481384	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28532174	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28759336	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35552143	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4737556	0.91[AFR][1000 genomes]
rs6471851	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471852	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471853	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471855	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471856	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471858	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];0.95[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]
rs6471859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471860	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6983247	0.82[CEU][hapmap]
rs6983830	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987786	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6988169	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6990370	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6998446	0.92[ASW][hapmap];0.96[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6998745	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7002077	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7002369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002846	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs7002871	0.82[AFR][1000 genomes]
rs7003287	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004004	0.91[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7006734	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7007157	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7009243	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7009482	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7463930	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463939	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7464181	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7464531	0.86[AFR][1000 genomes]
rs7812953	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7813357	0.87[AFR][1000 genomes]
rs7814280	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7814473	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7825247	0.89[AFR][1000 genomes]
rs7826329	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7832414	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs7832419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841372	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7841396	0.84[AFR][1000 genomes]
rs7841804	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7843385	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7845524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180936	0.87[YRI][hapmap]
rs9643367	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9643368	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv831333	chr8:61102862-61275122	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv890943	chr8:61134995-61225652	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6471857	CA8	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61164200-61186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:61167000-61177400	Weak transcription	Fetal Thymus	thymus
3	chr8:61167000-61180200	Weak transcription	Left Ventricle	heart
4	chr8:61167000-61193200	Weak transcription	Gastric	stomach
5	chr8:61167000-61193200	Weak transcription	Lung	lung
6	chr8:61167000-61193200	Weak transcription	Pancreas	Pancrea
7	chr8:61167600-61186400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr8:61170400-61178800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr8:61172600-61180600	Weak transcription	Placenta	Placenta
10	chr8:61172600-61185800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr8:61172800-61191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr8:61173000-61187600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr8:61174600-61178400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:61174600-61178800	Strong transcription	Fetal Intestine Large	intestine
15	chr8:61174600-61186600	Strong transcription	K562	blood
16	chr8:61175000-61178200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:61175000-61178200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr8:61175600-61177200	Strong transcription	Fetal Intestine Small	intestine
19	chr8:61176800-61178000	Strong transcription	Fetal Stomach	stomach
20	chr8:61176800-61178000	Strong transcription	A549	lung

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