Variant report

Variant	rs6877102
Chromosome Location	chr5:80770894-80770895
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:80757299..80759638-chr5:80770497..80773294,2	MCF-7	breast:
2	chr5:80763988..80765693-chr5:80769242..80771448,2	K562	blood:
3	chr5:80764193..80766521-chr5:80769242..80771330,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10035291	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10036712	0.82[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10041030	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10042201	0.82[CHB][hapmap]
rs10042303	0.91[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10043164	0.81[ASN][1000 genomes]
rs10056711	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068144	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10075648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942266	0.94[ASN][1000 genomes]
rs10942269	0.85[CHD][hapmap]
rs11739075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740689	0.85[CHD][hapmap]
rs11740719	0.92[CHB][hapmap]
rs11742106	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11949697	0.92[CHB][hapmap]
rs12153000	0.93[JPT][hapmap]
rs12697705	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13159500	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13171682	0.98[ASN][1000 genomes]
rs1541830	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162973	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396170	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34150522	0.81[ASN][1000 genomes]
rs34699788	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35224297	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792923	0.86[MEX][hapmap]
rs3805726	0.92[CHB][hapmap]
rs4274955	0.85[CHD][hapmap]
rs4392600	0.85[CHD][hapmap]
rs4513668	0.85[CHD][hapmap]
rs4529168	0.81[CHD][hapmap]
rs6452407	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452410	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452411	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6452412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452414	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6452415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452416	1.00[JPT][hapmap]
rs6865796	0.90[CEU][hapmap]
rs6866156	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866727	0.90[CEU][hapmap]
rs6866741	0.84[ASN][1000 genomes]
rs6868422	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868748	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872793	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874029	0.85[CHD][hapmap]
rs6874237	0.86[ASN][1000 genomes]
rs6874274	0.85[CHD][hapmap]
rs6878037	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6880200	0.84[JPT][hapmap]
rs6883488	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897189	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7702047	0.85[CHD][hapmap]
rs7702374	0.90[CEU][hapmap]
rs7711020	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719373	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725126	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733938	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7737895	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs9293275	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9596	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964102	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs9918175	0.90[CEU][hapmap]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:80735400-80778600	Weak transcription	Aorta	Aorta
3	chr5:80736000-80771200	Weak transcription	NHDF-Ad	bronchial
4	chr5:80739800-80773200	Strong transcription	Fetal Thymus	thymus
5	chr5:80745200-80771400	Weak transcription	Gastric	stomach
6	chr5:80748600-80771200	Weak transcription	Lung	lung
7	chr5:80758000-80774000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:80759600-80773200	Strong transcription	Dnd41	blood
9	chr5:80766200-80800000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:80766600-80771200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:80768600-80771000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:80768600-80771200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:80769200-80771000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:80769200-80771000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:80769200-80771000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:80769800-80771000	Strong transcription	Fetal Lung	lung
17	chr5:80769800-80771400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:80769800-80771400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:80769800-80771400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:80769800-80771400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:80769800-80771600	Weak transcription	Osteobl	bone
22	chr5:80769800-80772600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:80769800-80776400	Weak transcription	Pancreas	Pancrea
24	chr5:80769800-80778600	Weak transcription	K562	blood
25	chr5:80769800-80779600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:80770000-80771000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:80770000-80771000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:80770000-80771200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:80770000-80771200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:80770000-80771200	Weak transcription	HSMM	muscle
31	chr5:80770000-80771400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:80770000-80771400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:80770000-80771400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:80770000-80771600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:80770000-80771600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:80770000-80771600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:80770000-80771600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:80770000-80771600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:80770000-80771800	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:80770000-80771800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:80770000-80771800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:80770000-80771800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:80770000-80771800	Weak transcription	HSMMtube	muscle
44	chr5:80770000-80772000	Weak transcription	Fetal Intestine Large	intestine
45	chr5:80770000-80772000	Weak transcription	Placenta	Placenta
46	chr5:80770000-80772400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:80770000-80772800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:80770000-80773000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:80770000-80773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:80770000-80774400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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