Variant report

Variant	rs6896653
Chromosome Location	chr5:107704881-107704882
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:107704058..107705992-chr5:107711279..107713882,3	MCF-7	breast:
2	chr5:107703047..107709148-chr5:107715421..107721287,10	K562	blood:
3	chr5:107700578..107705838-chr5:107715421..107718628,5	K562	blood:
4	chr5:107703017..107709518-chr5:107714821..107720551,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10051605	0.86[JPT][hapmap]
rs10477419	0.86[JPT][hapmap]
rs10477892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10477895	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11742777	0.90[JPT][hapmap]
rs11747188	0.86[JPT][hapmap]
rs12655232	0.83[JPT][hapmap]
rs13153782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13161833	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13162374	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13162979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13173916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13190222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1355375	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421970	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1544741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158170	0.80[EUR][1000 genomes]
rs158604	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs158605	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs158606	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs158607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs158609	0.84[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs1588496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17161232	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17385448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17452232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1828457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1849012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1862196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2416189	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2416190	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs286764	0.82[CHB][hapmap]
rs286769	0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs286771	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2900034	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2900122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2941694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2966824	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2966830	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2966832	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2966834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34261817	0.85[EUR][1000 genomes]
rs34388	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs34409	0.83[EUR][1000 genomes]
rs34413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34420	0.81[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34421	0.83[EUR][1000 genomes]
rs34422	0.83[EUR][1000 genomes]
rs34527417	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34747859	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34771507	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34854088	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35903369	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4438862	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4957755	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[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]
rs4957756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62359544	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap]
rs6594299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6596770	0.82[CHB][hapmap]
rs6883082	0.82[CHB][hapmap]
rs71592749	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7713705	0.82[CHB][hapmap]
rs7721104	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7724056	0.83[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7726485	0.92[JPT][hapmap]
rs9326726	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs981755	0.84[JPT][hapmap]
rs988436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs988437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882688	chr5:107595383-107715746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107615000-107705600	Weak transcription	Left Ventricle	heart
2	chr5:107654600-107709400	Weak transcription	Pancreas	Pancrea
3	chr5:107658600-107709200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr5:107663800-107709400	Weak transcription	Primary T cells from cord blood	blood
5	chr5:107667600-107709200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:107668600-107706800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:107669200-107708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:107675000-107709200	Weak transcription	Fetal Thymus	thymus
9	chr5:107677800-107709200	Weak transcription	Ovary	ovary
10	chr5:107679200-107706800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:107679800-107705600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:107680000-107706800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:107680400-107707600	Weak transcription	Fetal Intestine Large	intestine
14	chr5:107688000-107707600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:107693000-107706800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:107693600-107706400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:107694400-107706800	Weak transcription	GM12878-XiMat	blood
18	chr5:107696600-107709200	Weak transcription	Fetal Lung	lung
19	chr5:107697000-107705000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:107697200-107715200	Weak transcription	HSMM	muscle
21	chr5:107697600-107705200	Weak transcription	Brain Substantia Nigra	brain
22	chr5:107697600-107706000	Weak transcription	Stomach Mucosa	stomach
23	chr5:107697600-107708000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:107697800-107707600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:107697800-107709200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:107698000-107707800	Weak transcription	Brain Anterior Caudate	brain
27	chr5:107698200-107715600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:107699000-107712800	Weak transcription	Right Ventricle	heart
29	chr5:107699600-107709200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:107700400-107707600	Weak transcription	Esophagus	oesophagus
31	chr5:107700600-107707600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:107700600-107707600	Weak transcription	NHDF-Ad	bronchial
33	chr5:107700600-107709000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:107700600-107709400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:107700800-107707600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:107701000-107709400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:107701200-107706000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:107701200-107706400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:107701200-107707600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:107701200-107709000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:107701200-107709400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:107702600-107709200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr5:107702600-107709200	Weak transcription	Psoas Muscle	Psoas
44	chr5:107702800-107705600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:107702800-107707600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:107702800-107708200	Weak transcription	Fetal Kidney	kidney
47	chr5:107703000-107707000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:107703000-107707400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:107703200-107707800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr5:107703400-107705600	Weak transcription	Liver	Liver

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