Variant report

Variant	rs637868
Chromosome Location	chr1:120257110-120257111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:119682953..119685803-chr1:120256738..120259239,2	K562	blood:
2	chr1:120188760..120191651-chr1:120254416..120257641,3	K562	blood:
3	chr1:120188760..120191459-chr1:120254916..120257641,2	K562	blood:
4	chr1:120186762..120190857-chr1:120254727..120257522,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116874	Chromatin interaction
ENSG00000231365	Chromatin interaction
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2764886	0.86[JPT][hapmap]
rs477992	0.86[JPT][hapmap]
rs478093	0.86[JPT][hapmap]
rs483180	0.86[JPT][hapmap]
rs561931	0.86[JPT][hapmap]
rs592762	0.86[JPT][hapmap]
rs611365	0.86[JPT][hapmap]
rs662602	0.86[JPT][hapmap]
rs666930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs637868	FAM46C	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120254800-120257400	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr1:120255400-120257200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:120255400-120257200	Flanking Active TSS	Fetal Muscle Leg	muscle
4	chr1:120255600-120257200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:120255600-120257200	Flanking Active TSS	Fetal Intestine Small	intestine
6	chr1:120255600-120257200	Flanking Active TSS	Fetal Lung	lung
7	chr1:120255600-120257200	Flanking Active TSS	K562	blood
8	chr1:120255600-120257400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr1:120255600-120257600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:120255600-120257600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:120255600-120258400	Weak transcription	Right Ventricle	heart
12	chr1:120255800-120257200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:120255800-120257200	Flanking Active TSS	Fetal Intestine Large	intestine
14	chr1:120255800-120257400	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr1:120255800-120257400	Transcr. at gene 5' and 3'	NHEK	skin
16	chr1:120255800-120257600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:120255800-120259400	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr1:120256000-120257200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:120256000-120257400	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
20	chr1:120256000-120257600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:120256000-120257600	Enhancers	Placenta	Placenta
22	chr1:120256000-120258800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:120256000-120258800	Enhancers	Ovary	ovary
24	chr1:120256000-120259000	Enhancers	Adipose Nuclei	Adipose
25	chr1:120256000-120259400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
26	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:120256200-120257400	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:120256200-120257400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:120256200-120257600	Enhancers	Fetal Brain Male	brain
30	chr1:120256200-120258000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:120256200-120259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:120256200-120266600	Weak transcription	Primary B cells from cord blood	blood
33	chr1:120256200-120267400	Weak transcription	Lung	lung
34	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:120256400-120257200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:120256400-120257400	Weak transcription	Brain Angular Gyrus	brain
37	chr1:120256400-120257400	Flanking Active TSS	HepG2	liver
38	chr1:120256400-120258000	Enhancers	Brain Hippocampus Middle	brain
39	chr1:120256400-120258200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:120256400-120258200	Weak transcription	Right Atrium	heart
41	chr1:120256400-120258600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:120256400-120259200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:120256400-120259400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:120256400-120259600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:120256400-120271800	Weak transcription	Gastric	stomach
46	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
48	chr1:120256600-120257200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:120256600-120257200	Active TSS	Brain Anterior Caudate	brain
50	chr1:120256600-120257200	Flanking Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links