Variant report

Variant	rs6905061
Chromosome Location	chr6:107079560-107079561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:107079420-107079879	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:107074696..107076514-chr6:107078215..107079891,2	K562	blood:
2	chr6:107069824..107071669-chr6:107079166..107080707,2	K562	blood:

Variant related genes	Relation type
RTN4IP1	TF binding region

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10499045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12110543	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111259	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12663879	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1824619	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2035152	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2035153	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2035154	0.87[ASN][1000 genomes]
rs2035155	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2353040	0.87[ASN][1000 genomes]
rs3747791	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946769	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4946771	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4946772	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4946773	0.87[ASN][1000 genomes]
rs59238907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6568446	0.87[ASN][1000 genomes]
rs6900830	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6900886	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6905519	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6906495	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6914497	0.87[ASN][1000 genomes]
rs6916265	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6919395	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6923868	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6925367	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6925512	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6933064	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613231	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613232	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613233	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613234	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613235	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613236	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613237	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613238	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613241	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7454323	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7748400	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759021	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9372137	0.87[ASN][1000 genomes]
rs9373881	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107076200-107080600	Active TSS	GM12878-XiMat	blood
2	chr6:107078000-107084800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:107078000-107090000	Weak transcription	Aorta	Aorta
4	chr6:107078200-107082400	Weak transcription	Lung	lung
5	chr6:107078200-107084800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:107078400-107079600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr6:107078400-107080000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:107078400-107080000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:107078400-107085000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:107078400-107090400	Weak transcription	HSMMtube	muscle
11	chr6:107078600-107079600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:107078600-107079600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:107078600-107079600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:107078600-107079600	Enhancers	Osteobl	bone
15	chr6:107078600-107080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:107078600-107080400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:107078600-107084400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:107078600-107084400	Weak transcription	Left Ventricle	heart
19	chr6:107078600-107084400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:107078600-107084600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:107078600-107084800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:107078600-107084800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:107078600-107084800	Weak transcription	Fetal Thymus	thymus
24	chr6:107078600-107084800	Weak transcription	Right Atrium	heart
25	chr6:107078600-107084800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:107078600-107084800	Weak transcription	Small Intestine	intestine
27	chr6:107078600-107085000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:107078600-107085000	Weak transcription	Liver	Liver
29	chr6:107078600-107085000	Weak transcription	Thymus	Thymus
30	chr6:107078600-107085200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:107078600-107085400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:107078600-107086000	Weak transcription	Primary T cells from cord blood	blood
33	chr6:107078600-107086400	Weak transcription	Psoas Muscle	Psoas
34	chr6:107078600-107086600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:107078600-107086600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:107078600-107087400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:107078600-107087800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:107078600-107088000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:107078600-107088000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:107078600-107088200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:107078600-107089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:107078600-107089000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:107078600-107089400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:107078600-107089600	Weak transcription	Fetal Intestine Small	intestine
45	chr6:107078600-107089800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:107078600-107090000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:107078600-107090000	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:107078600-107090000	Weak transcription	Fetal Stomach	stomach
49	chr6:107078600-107090000	Weak transcription	Right Ventricle	heart
50	chr6:107078600-107090200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links