Variant report

Variant	rs968839
Chromosome Location	chr6:107008430-107008431
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	chr6:106895041..106897753-chr6:107007348..107009765,2	MCF-7	breast:
2	chr6:107002175..107004858-chr6:107006696..107008567,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202386	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1676009	0.85[AMR][1000 genomes]
rs1676011	0.85[AMR][1000 genomes]
rs1676012	0.85[AMR][1000 genomes]
rs1676014	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1676015	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1676017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1770727	0.85[AMR][1000 genomes]
rs1770729	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1770730	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1981308	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2353041	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4946769	0.94[AFR][1000 genomes]
rs4946771	0.93[AFR][1000 genomes]
rs4946772	0.88[AFR][1000 genomes]
rs6568446	0.90[AFR][1000 genomes]
rs6914497	0.86[AFR][1000 genomes]
rs7749873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9372137	0.86[AFR][1000 genomes]
rs9373878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9373881	0.90[AFR][1000 genomes]
rs963683	1.00[AFR][1000 genomes];1.00[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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
2	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
4	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:106994200-107009000	Weak transcription	Left Ventricle	heart
6	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:106995000-107019400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:106995200-107016200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:106995200-107018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:106996200-107017200	Weak transcription	HSMM	muscle
12	chr6:106996200-107018400	Weak transcription	Fetal Stomach	stomach
13	chr6:106996200-107022400	Weak transcription	Ovary	ovary
14	chr6:106996200-107023000	Weak transcription	Stomach Mucosa	stomach
15	chr6:106996400-107009000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:106996400-107012200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:106996400-107027000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
20	chr6:106996600-107009200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:106996600-107009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:106996600-107012000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:106996600-107018400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:106996600-107022400	Weak transcription	HUVEC	blood vessel
25	chr6:106999000-107022400	Weak transcription	Right Ventricle	heart
26	chr6:106999200-107022400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:107000400-107018800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:107000800-107021200	Strong transcription	Primary B cells from cord blood	blood
30	chr6:107001200-107014600	Strong transcription	GM12878-XiMat	blood
31	chr6:107001400-107018600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:107002000-107010000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:107002000-107011400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:107002000-107016000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:107002200-107008800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:107002200-107019000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:107002200-107020200	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:107002200-107020200	Weak transcription	Pancreas	Pancrea
39	chr6:107002400-107023000	Weak transcription	Gastric	stomach
40	chr6:107002800-107011600	Weak transcription	Spleen	Spleen
41	chr6:107002800-107017400	Weak transcription	Lung	lung
42	chr6:107003600-107011800	Strong transcription	Fetal Thymus	thymus
43	chr6:107003800-107010400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:107003800-107019400	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:107004000-107015800	Weak transcription	Esophagus	oesophagus
46	chr6:107004200-107009600	Strong transcription	Placenta	Placenta
47	chr6:107004200-107016000	Weak transcription	Colonic Mucosa	Colon
48	chr6:107004600-107012000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:107005000-107018800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:107005000-107021400	Weak transcription	Stomach Smooth Muscle	stomach

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