Variant report

Variant	rs6686076
Chromosome Location	chr1:161013312-161013313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
2	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
3	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
4	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
5	chr1:161011663..161014033-chr1:161014079..161015803,2	K562	blood:
6	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
7	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:

Variant related genes	Relation type
ENSG00000158773	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000162755	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12036299	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1556259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832617	0.87[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs1974140	0.92[EUR][1000 genomes]
rs2073653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766382	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766383	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4617422	1.00[CEU][hapmap]
rs57839241	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58318788	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs58974723	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6427572	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660240	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6695707	0.87[TSI][hapmap]
rs6701822	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7516231	1.00[CEU][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6686076	F11R	cis	cerebellum	SCAN
rs6686076	ITLN1	cis	cerebellum	SCAN
rs6686076	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs6686076	SNORA42	cis	cerebellum	SCAN
rs6686076	TSTD1	cis	lymphoblastoid	seeQTL
rs6686076	SDHC	cis	parietal	SCAN
rs6686076	FCGR2A	cis	parietal	SCAN
rs6686076	ASH1L	cis	cerebellum	SCAN
rs6686076	ARHGEF11	cis	cerebellum	SCAN
rs6686076	OR10K1	cis	cerebellum	SCAN
rs6686076	KCNJ9	cis	cerebellum	SCAN
rs6686076	KIRREL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:161008800-161013400	Strong transcription	Brain Cingulate Gyrus	brain
9	chr1:161008800-161014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:161009000-161013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:161009000-161013400	Strong transcription	Fetal Stomach	stomach
12	chr1:161009000-161014000	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr1:161009200-161013400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:161009200-161013400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:161009200-161013400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:161009200-161013400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:161009200-161013400	Strong transcription	Brain Angular Gyrus	brain
18	chr1:161009200-161013400	Strong transcription	Brain Anterior Caudate	brain
19	chr1:161009200-161013400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:161009400-161013400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:161009400-161013400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:161009400-161013400	Strong transcription	HMEC	breast
23	chr1:161009400-161013400	Strong transcription	K562	blood
24	chr1:161009400-161014000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:161009600-161013400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:161009600-161013400	Strong transcription	Placenta	Placenta
27	chr1:161009600-161013400	Strong transcription	HSMM	muscle
28	chr1:161009800-161013400	Strong transcription	Fetal Lung	lung
29	chr1:161009800-161013800	Genic enhancers	Dnd41	blood
30	chr1:161010000-161013400	Strong transcription	Colonic Mucosa	Colon
31	chr1:161010000-161013400	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:161010600-161014000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:161010600-161014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:161011000-161013400	Genic enhancers	Primary B cells from cord blood	blood
35	chr1:161011200-161013400	Genic enhancers	Fetal Thymus	thymus
36	chr1:161011600-161013400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:161012000-161013400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:161012000-161014200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:161012000-161014600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:161012200-161013600	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:161012400-161014200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:161012600-161013400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:161012600-161014000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:161012600-161014000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:161012600-161014400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:161012600-161014400	Weak transcription	Ovary	ovary
47	chr1:161012800-161013400	Genic enhancers	Adipose Nuclei	Adipose
48	chr1:161012800-161013400	Strong transcription	Spleen	Spleen
49	chr1:161012800-161014000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:161012800-161014000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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