Variant report

Variant	rs1770727
Chromosome Location	chr6:106999550-106999551
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	chr6:106990837..106993931-chr6:106996769..107001251,4	K562	blood:
2	chr6:106991231..106993134-chr6:106999067..107001251,2	K562	blood:

Variant related genes	Relation type
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1676007	0.86[AMR][1000 genomes]
rs1676009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1676011	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1676012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1676013	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1676014	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs1676015	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs1676017	0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs1676029	0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1676030	0.83[AFR][1000 genomes]
rs1770724	0.93[AMR][1000 genomes]
rs1770725	0.93[AMR][1000 genomes]
rs1770729	1.00[AMR][1000 genomes]
rs1770730	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs2353041	0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs4946767	0.82[MEX][hapmap]
rs4946769	0.85[MKK][hapmap];0.83[YRI][hapmap]
rs4946771	0.83[YRI][hapmap]
rs4946773	0.83[YRI][hapmap]
rs6568446	0.83[YRI][hapmap]
rs6914497	0.83[YRI][hapmap]
rs6936524	0.82[MEX][hapmap]
rs6938201	0.83[YRI][hapmap]
rs7749873	0.85[AMR][1000 genomes]
rs7759505	0.82[MEX][hapmap]
rs9373878	0.85[AMR][1000 genomes]
rs963683	0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs968839	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS 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	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
3	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
5	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
7	chr6:106988200-107001400	Weak transcription	Lung	lung
8	chr6:106991200-106999600	Strong transcription	Dnd41	blood
9	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:106994200-107000200	Weak transcription	Esophagus	oesophagus
11	chr6:106994200-107009000	Weak transcription	Left Ventricle	heart
12	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:106994400-107000800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:106994600-106999600	Strong transcription	GM12878-XiMat	blood
16	chr6:106994600-107001400	Weak transcription	Spleen	Spleen
17	chr6:106994800-107000800	Weak transcription	Liver	Liver
18	chr6:106994800-107004200	Strong transcription	Primary T cells from cord blood	blood
19	chr6:106994800-107004600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:106994800-107004600	Weak transcription	Hela-S3	cervix
21	chr6:106995000-107019400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:106995200-107002000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:106995200-107016200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:106995200-107018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:106995800-107001400	Weak transcription	Thymus	Thymus
26	chr6:106995800-107003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:106995800-107004400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr6:106996000-107000800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:106996000-107000800	Weak transcription	Adipose Nuclei	Adipose
30	chr6:106996000-107003400	Weak transcription	Colonic Mucosa	Colon
31	chr6:106996200-107001400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:106996200-107002000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:106996200-107017200	Weak transcription	HSMM	muscle
34	chr6:106996200-107018400	Weak transcription	Fetal Stomach	stomach
35	chr6:106996200-107022400	Weak transcription	Ovary	ovary
36	chr6:106996200-107023000	Weak transcription	Stomach Mucosa	stomach
37	chr6:106996400-107000000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:106996400-107000800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:106996400-107001400	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:106996400-107001600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:106996400-107005600	Weak transcription	Osteobl	bone
42	chr6:106996400-107009000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:106996400-107012200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:106996400-107027000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
47	chr6:106996600-107000800	Weak transcription	Fetal Intestine Large	intestine
48	chr6:106996600-107000800	Weak transcription	Fetal Thymus	thymus
49	chr6:106996600-107000800	Weak transcription	HepG2	liver
50	chr6:106996600-107000800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links