Variant report

Variant	rs7756
Chromosome Location	chr1:186281696-186281697
allele	G/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	chr1:186277800-186282438	K562	blood:	n/a	n/a
2	POLR2A	chr1:186281350-186282269	A549	lung:	n/a	n/a
3	POLR2A	chr1:186281544-186282146	K562	blood:	n/a	n/a
4	POLR2A	chr1:186281277-186282317	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:186281260-186282142	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186279942..186281845-chr1:186343325..186346234,2	K562	blood:

Variant related genes	Relation type
RNU6-1240P	TF binding region
ENSG00000047410	Chromatin interaction
ENSG00000157181	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494586	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10911855	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16825295	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[ASN][1000 genomes]
rs1919198	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026187	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2037830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141393	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2178215	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2383476	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3115761	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3124814	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131550	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131551	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766708	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766709	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425026	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657726	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700930	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs878041	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8824	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7756	C1orf27	cis	cerebellum	SCAN
rs7756	OCLM	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186272000-186306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:186273200-186283800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:186273200-186284000	Weak transcription	Spleen	Spleen
4	chr1:186273200-186286200	Weak transcription	Pancreas	Pancrea
5	chr1:186273200-186290000	Weak transcription	Gastric	stomach
6	chr1:186275000-186282800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:186275000-186284000	Weak transcription	Aorta	Aorta
8	chr1:186275000-186284000	Weak transcription	Esophagus	oesophagus
9	chr1:186275000-186284000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:186275000-186284000	Weak transcription	Lung	lung
11	chr1:186275000-186284000	Weak transcription	Right Ventricle	heart
12	chr1:186275000-186284800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:186275000-186286200	Weak transcription	Psoas Muscle	Psoas
14	chr1:186275200-186284000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:186275600-186283600	Weak transcription	HSMMtube	muscle
16	chr1:186276400-186281800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:186276800-186284800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:186276800-186285800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:186277000-186283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:186277600-186295200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:186277600-186342600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:186277800-186297000	Strong transcription	Primary B cells from cord blood	blood
23	chr1:186278000-186284000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:186278000-186284000	Weak transcription	Fetal Stomach	stomach
25	chr1:186278000-186284000	Weak transcription	Thymus	Thymus
26	chr1:186278200-186281800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:186278200-186281800	Weak transcription	K562	blood
28	chr1:186278200-186284000	Weak transcription	Ovary	ovary
29	chr1:186278200-186284000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:186278400-186284000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:186278400-186284000	Weak transcription	Fetal Intestine Small	intestine
32	chr1:186278400-186342600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:186278600-186292800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:186278800-186320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:186279200-186284200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:186279400-186281800	Weak transcription	Colonic Mucosa	Colon
37	chr1:186279400-186295800	Strong transcription	A549	lung
38	chr1:186279400-186342400	Strong transcription	Fetal Thymus	thymus
39	chr1:186279600-186282400	Strong transcription	Primary T cells from cord blood	blood
40	chr1:186279600-186283600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:186279600-186284000	Weak transcription	Small Intestine	intestine
42	chr1:186279600-186284800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:186279600-186292200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:186279600-186317600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:186279600-186342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:186279800-186282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:186279800-186283400	Weak transcription	NHLF	lung
48	chr1:186280000-186284000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:186280000-186285600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:186280000-186317600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links