Variant report

Variant	rs6743866
Chromosome Location	chr2:9986869-9986870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9983066..9987186-chr2:10091615..10095343,4	MCF-7	breast:
2	chr2:9985865..9987759-chr2:9990520..9994621,3	MCF-7	breast:
3	chr2:9985747..9988019-chr2:10062440..10064881,2	MCF-7	breast:
4	chr2:9986181..9988070-chr2:9991011..9993550,2	MCF-7	breast:
5	chr2:9981404..9986079-chr2:9986481..9992681,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1014509	0.87[AFR][1000 genomes]
rs10929617	0.87[AFR][1000 genomes]
rs12470216	0.87[AFR][1000 genomes]
rs12611655	0.87[AFR][1000 genomes]
rs12613533	0.87[AFR][1000 genomes]
rs12617615	0.87[AFR][1000 genomes]
rs12621415	0.87[AFR][1000 genomes]
rs12622420	0.87[AFR][1000 genomes]
rs12623017	0.87[AFR][1000 genomes]
rs1473962	0.87[AFR][1000 genomes]
rs16867195	0.87[AFR][1000 genomes]
rs16867196	0.87[AFR][1000 genomes]
rs16867211	0.87[AFR][1000 genomes]
rs4143791	0.87[AFR][1000 genomes]
rs4143793	0.93[AFR][1000 genomes]
rs4610025	0.87[AFR][1000 genomes]
rs4627538	0.93[AFR][1000 genomes]
rs4669472	0.87[AFR][1000 genomes]
rs4669473	0.87[AFR][1000 genomes]
rs4669475	0.83[AFR][1000 genomes]
rs4669476	0.87[AFR][1000 genomes]
rs4669478	0.87[AFR][1000 genomes]
rs62127129	0.89[AFR][1000 genomes]
rs62127130	0.87[AFR][1000 genomes]
rs62127137	0.87[AFR][1000 genomes]
rs62127138	0.87[AFR][1000 genomes]
rs62127564	0.87[AFR][1000 genomes]
rs62127565	0.87[AFR][1000 genomes]
rs6707551	0.81[AFR][1000 genomes]
rs6713616	0.95[EUR][1000 genomes]
rs6743707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6753379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72782635	0.87[AFR][1000 genomes]
rs7559653	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563385	0.87[AFR][1000 genomes]
rs7579559	0.87[AFR][1000 genomes]
rs7608055	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984200-9994000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:9984400-9987400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:9984600-9990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:9984600-9992600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:9984600-9995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:9984800-9997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
8	chr2:9985000-9987200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:9985000-9987200	Weak transcription	Psoas Muscle	Psoas
10	chr2:9985000-9990400	Weak transcription	Brain Angular Gyrus	brain
11	chr2:9985000-9990800	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:9985000-9991000	Weak transcription	Colonic Mucosa	Colon
13	chr2:9985000-9992000	Weak transcription	Brain Substantia Nigra	brain
14	chr2:9985000-9992000	Weak transcription	Lung	lung
15	chr2:9985000-9992000	Weak transcription	Ovary	ovary
16	chr2:9985000-9992200	Weak transcription	Fetal Stomach	stomach
17	chr2:9985000-9992200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:9985000-9993600	Weak transcription	Right Ventricle	heart
19	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:9985200-9987200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:9985200-9987800	Genic enhancers	Dnd41	blood
22	chr2:9985200-9987800	Enhancers	Hela-S3	cervix
23	chr2:9985200-9987800	Enhancers	HMEC	breast
24	chr2:9985200-9987800	Genic enhancers	Osteobl	bone
25	chr2:9985200-9989600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:9985200-9995600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:9985200-9997200	Weak transcription	Fetal Heart	heart
28	chr2:9985400-9987000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:9985400-9987000	Genic enhancers	K562	blood
30	chr2:9985400-9987200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr2:9985400-9987600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:9985400-9987600	Enhancers	NH-A	brain
33	chr2:9985400-9988200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:9985400-9988400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:9985400-9989800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:9985400-9993800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:9985400-9995400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:9985400-9995400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:9985400-9995400	Weak transcription	Small Intestine	intestine
40	chr2:9985600-9987400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:9985600-9987400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:9985600-9987800	Strong transcription	Adipose Nuclei	Adipose
43	chr2:9985600-9987800	Strong transcription	Brain Anterior Caudate	brain
44	chr2:9985600-9987800	Strong transcription	HSMM	muscle
45	chr2:9985600-9988200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:9985600-9988200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:9985600-9989200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:9985600-9989600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:9985600-9989800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:9985600-9990600	Weak transcription	HSMMtube	muscle

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