Variant report

Variant	rs16878734
Chromosome Location	chr6:87943281-87943282
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87863356..87867363-chr6:87942975..87946448,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188994	Chromatin interaction
ENSG00000272008	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10488045	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10498960	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878473	0.82[EUR][1000 genomes]
rs16878570	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878622	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878638	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878712	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16878713	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16878729	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs16878736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878809	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16878856	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878863	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878942	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878991	0.82[AFR][1000 genomes]
rs16878999	0.82[AFR][1000 genomes]
rs1925693	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41273281	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41273283	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55647962	0.91[EUR][1000 genomes]
rs56096438	0.82[EUR][1000 genomes]
rs56193950	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56305030	0.82[AFR][1000 genomes]
rs56678817	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56743579	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56847789	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56999910	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs57043501	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57116567	0.94[EUR][1000 genomes]
rs57217108	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs57421283	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57552196	0.82[AFR][1000 genomes]
rs57607342	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs57962992	0.91[EUR][1000 genomes]
rs58124219	0.82[EUR][1000 genomes]
rs58269367	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58327183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58474842	1.00[EUR][1000 genomes]
rs58576901	0.82[EUR][1000 genomes]
rs58731649	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58735749	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58751410	0.91[EUR][1000 genomes]
rs59034165	0.82[EUR][1000 genomes]
rs59138817	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59150116	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59214037	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59344869	0.84[AFR][1000 genomes]
rs59495279	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs59654654	0.94[EUR][1000 genomes]
rs59875769	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60074363	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60285195	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60544317	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60746078	0.82[EUR][1000 genomes]
rs60845773	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60985818	0.87[EUR][1000 genomes]
rs60994855	0.91[EUR][1000 genomes]
rs61047847	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs61379368	1.00[EUR][1000 genomes]
rs61705669	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483720	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483728	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483743	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483749	1.00[EUR][1000 genomes]
rs73483752	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483758	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483760	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483765	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483769	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483771	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73483774	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483790	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483796	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73483799	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485808	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485813	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485826	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485828	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485831	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485848	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485849	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73499768	0.82[EUR][1000 genomes]
rs73499770	0.82[EUR][1000 genomes]
rs73499771	0.82[EUR][1000 genomes]
rs73499800	0.94[EUR][1000 genomes]
rs73499802	0.94[EUR][1000 genomes]
rs73501611	0.91[EUR][1000 genomes]
rs73501620	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501623	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501629	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501632	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501636	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501638	0.94[EUR][1000 genomes]
rs73501641	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501658	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73501662	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73751992	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87884000-87964400	Weak transcription	NHEK	skin
2	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
3	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:87905200-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:87906200-87956200	Weak transcription	A549	lung
6	chr6:87906400-87964400	Weak transcription	NHLF	lung
7	chr6:87910600-87956000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:87920000-87945400	Strong transcription	Dnd41	blood
9	chr6:87922200-87956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:87923200-87953600	Weak transcription	Stomach Mucosa	stomach
11	chr6:87923200-87956000	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:87923400-87955600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:87923400-87956200	Weak transcription	Gastric	stomach
14	chr6:87923400-87956200	Weak transcription	Small Intestine	intestine
15	chr6:87923400-87969000	Weak transcription	Psoas Muscle	Psoas
16	chr6:87924000-87956200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:87924400-87966000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:87924600-87956200	Weak transcription	Right Ventricle	heart
19	chr6:87925600-87948200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:87928000-87956200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:87930600-87954000	Weak transcription	HMEC	breast
22	chr6:87931200-87952400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:87933200-87956200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:87933400-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:87933600-87945000	Weak transcription	Fetal Intestine Small	intestine
26	chr6:87933600-87948000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:87933600-87948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:87933600-87948600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:87933600-87948600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:87933600-87948800	Weak transcription	Ovary	ovary
31	chr6:87933600-87949600	Weak transcription	Fetal Stomach	stomach
32	chr6:87933600-87951200	Weak transcription	Pancreas	Pancrea
33	chr6:87933600-87956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:87933600-87956200	Weak transcription	Lung	lung
35	chr6:87933600-87956400	Weak transcription	Esophagus	oesophagus
36	chr6:87933800-87944600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:87933800-87956200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:87933800-87956200	Weak transcription	Colonic Mucosa	Colon
39	chr6:87934000-87947000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:87934000-87948800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:87934000-87956200	Weak transcription	Left Ventricle	heart
42	chr6:87934000-87956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:87934200-87946400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:87934200-87954600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:87934400-87953400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:87934400-87955600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr6:87934600-87943400	Weak transcription	HSMM	muscle
48	chr6:87934600-87944400	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:87934600-87953600	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:87934600-87964200	Weak transcription	Rectal Smooth Muscle	rectum

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