Variant report

Variant	rs6671492
Chromosome Location	chr1:161038767-161038768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161013921..161016040-chr1:161036662..161039623,2	MCF-7	breast:
2	chr1:161038232..161039779-chr1:161100703..161102349,2	K562	blood:
3	chr1:160969057..160971514-chr1:161037864..161040165,2	K562	blood:
4	chr1:161037367..161040150-chr1:161043095..161044825,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158773	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000143217	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10797092	0.84[CHD][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908822	0.82[AMR][1000 genomes]
rs11265547	0.82[AMR][1000 genomes]
rs11265548	0.81[MKK][hapmap]
rs11265549	0.83[JPT][hapmap]
rs12118313	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12401309	0.84[JPT][hapmap]
rs1467742	0.84[JPT][hapmap]
rs1556257	0.84[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs3820097	0.84[JPT][hapmap]
rs3892376	0.84[JPT][hapmap]
rs4233364	0.84[JPT][hapmap]
rs4396136	0.82[YRI][hapmap]
rs4656285	0.85[AMR][1000 genomes]
rs4656978	0.83[GIH][hapmap];0.94[MEX][hapmap];0.83[AMR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6671492	F11R	cis	cerebellum	SCAN
rs6671492	RXFP4	cis	parietal	SCAN
rs6671492	DEDD	cis	cerebellum	SCAN
rs6671492	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs6671492	NDUFS2	cis	parietal	SCAN
rs6671492	TSTD1	cis	Artery Tibial	GTEx
rs6671492	F11R	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161026400-161039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:161030000-161046200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:161036600-161039600	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:161036600-161040200	Enhancers	K562	blood
5	chr1:161036800-161040200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:161037200-161038800	Flanking Active TSS	Dnd41	blood
7	chr1:161037400-161039000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
8	chr1:161037400-161040200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr1:161037400-161040200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:161037400-161040200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:161037600-161039600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:161037600-161040200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:161037800-161038800	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr1:161037800-161039200	Active TSS	Adipose Nuclei	Adipose
15	chr1:161037800-161039200	Flanking Active TSS	Fetal Thymus	thymus
16	chr1:161037800-161039600	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:161037800-161039800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:161037800-161039800	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:161038000-161039400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:161038000-161039600	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:161038000-161039600	Enhancers	Stomach Mucosa	stomach
22	chr1:161038000-161039800	Active TSS	Primary T cells fromperipheralblood	blood
23	chr1:161038000-161039800	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr1:161038000-161039800	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:161038000-161039800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:161038000-161039800	Active TSS	Fetal Intestine Small	intestine
27	chr1:161038000-161039800	Active TSS	GM12878-XiMat	blood
28	chr1:161038200-161038800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:161038200-161039000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:161038200-161039000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:161038200-161039000	Weak transcription	Right Atrium	heart
32	chr1:161038200-161039800	Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:161038200-161039800	Active TSS	Primary B cells from peripheral blood	blood
34	chr1:161038200-161039800	Active TSS	Primary T cells from cord blood	blood
35	chr1:161038200-161039800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:161038200-161039800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:161038200-161039800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr1:161038200-161039800	Active TSS	Fetal Muscle Leg	muscle
39	chr1:161038200-161039800	Active TSS	Thymus	Thymus
40	chr1:161038200-161040000	Active TSS	Duodenum Mucosa	Duodenum
41	chr1:161038200-161040000	Enhancers	NHEK	skin
42	chr1:161038400-161039000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:161038400-161039200	Active TSS	Colon Smooth Muscle	Colon
44	chr1:161038400-161039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:161038400-161039600	Active TSS	Brain Anterior Caudate	brain
46	chr1:161038400-161039600	Bivalent/Poised TSS	Fetal Stomach	stomach
47	chr1:161038400-161039800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:161038400-161039800	Active TSS	Liver	Liver
49	chr1:161038400-161039800	Transcr. at gene 5' and 3'	Placenta	Placenta
50	chr1:161038400-161039800	Active TSS	Small Intestine	intestine

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