Variant report

Variant	rs2677760
Chromosome Location	chr3:178903264-178903265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178896021..178899660-chr3:178900904..178904164,4	K562	blood:
2	chr3:178802128..178803691-chr3:178902292..178905279,2	MCF-7	breast:
3	chr3:178898160..178900976-chr3:178901666..178903620,2	K562	blood:
4	chr3:178891781..178894758-chr3:178901909..178904636,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1607237	0.94[JPT][hapmap];0.80[MEX][hapmap]
rs2459693	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs2699888	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2699895	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2699896	0.86[AMR][1000 genomes]
rs3729679	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7650873	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs870995	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861291	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv963506	chr3:178897583-178904531	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv524471	chr3:178897674-178903264	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2677760	FAM131A	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178883800-178905800	Weak transcription	Fetal Kidney	kidney
2	chr3:178887200-178912000	Weak transcription	Thymus	Thymus
3	chr3:178894200-178905800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:178894400-178903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:178895600-178904400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:178896200-178903600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:178896400-178905000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:178896600-178904200	Enhancers	Colon Smooth Muscle	Colon
9	chr3:178896800-178912200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:178896800-178912400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:178897600-178904600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:178897800-178906800	Weak transcription	Fetal Stomach	stomach
13	chr3:178897800-178919400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:178898600-178903400	Enhancers	Adipose Nuclei	Adipose
15	chr3:178899000-178907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:178899000-178907600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:178899200-178903600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:178899200-178906200	Weak transcription	Fetal Heart	heart
19	chr3:178899200-178907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:178899200-178907400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:178899200-178951800	Weak transcription	K562	blood
22	chr3:178899600-178904000	Weak transcription	HUVEC	blood vessel
23	chr3:178900000-178905800	Weak transcription	GM12878-XiMat	blood
24	chr3:178900000-178929800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:178900200-178904000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:178900400-178912200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:178900400-178912400	Weak transcription	NH-A	brain
28	chr3:178900600-178903400	Weak transcription	Right Ventricle	heart
29	chr3:178900600-178903600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:178900600-178903600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:178900600-178904000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:178900600-178904000	Weak transcription	HMEC	breast
33	chr3:178900600-178904000	Weak transcription	HSMMtube	muscle
34	chr3:178900600-178905800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:178900600-178905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:178900600-178905800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:178900600-178906000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:178900600-178906800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:178900600-178907200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:178900600-178912000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:178900600-178912000	Weak transcription	Left Ventricle	heart
42	chr3:178900600-178912200	Weak transcription	Pancreas	Pancrea
43	chr3:178900800-178903800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:178900800-178904000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:178900800-178904000	Weak transcription	Brain Anterior Caudate	brain
46	chr3:178900800-178904000	Weak transcription	HSMM	muscle
47	chr3:178900800-178907800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:178900800-178912400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:178900800-178913400	Weak transcription	Osteobl	bone
50	chr3:178901000-178904000	Weak transcription	Muscle Satellite Cultured Cells	--

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