Variant report

Variant	rs2245702
Chromosome Location	chr1:179711825-179711826
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	E2F6	chr1:179711602-179713485	H1-hESC	embryonic stem cell:	n/a	chr1:179712478-179712488 chr1:179712734-179712743 chr1:179713026-179713035
2	MAX	chr1:179711632-179713229	H1-hESC	embryonic stem cell:	n/a	chr1:179713027-179713037 chr1:179713049-179713059
3	REST	chr1:179711790-179712373	H1-neurons	neurons:	n/a	chr1:179712330-179712350
4	MAX	chr1:179711756-179712391	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr1:179711668-179713276	H1-hESC	embryonic stem cell:	n/a	chr1:179713027-179713037 chr1:179713049-179713059
6	E2F6	chr1:179711694-179713203	H1-hESC	embryonic stem cell:	n/a	chr1:179712478-179712488 chr1:179712734-179712743 chr1:179713026-179713035
7	POLR2A	chr1:179711779-179712384	H1-neurons	neurons:	n/a	n/a
8	SUZ12	chr1:179711443-179714153	NT2-D1	testis:	n/a	n/a
9	SIN3A	chr1:179711528-179712544	H1-hESC	embryonic stem cell:	n/a	chr1:179712163-179712177
10	MXI1	chr1:179710798-179717112	SK-N-SH	brain:	n/a	n/a
11	SUZ12	chr1:179711517-179714476	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM163A-1	chr1:179711490-179711832	ENSG00000243062.1
2	lnc-FAM163A-1	chr1:179711490-179711832	ENSG00000243062.1
3	lnc-FAM163A-1	chr1:179711490-179711844	NONHSAT008204

Variant related genes	Relation type
FAM163A	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1052447	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10798718	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10798719	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs10798720	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs10798721	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs10913874	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10913875	0.90[CHB][hapmap]
rs10913876	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs10913877	0.85[ASN][1000 genomes]
rs10913878	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs10913879	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs11578918	0.90[CHB][hapmap]
rs11588754	0.95[ASN][1000 genomes]
rs12047821	0.84[ASN][1000 genomes]
rs12408874	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs12408882	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs16854629	0.90[CHB][hapmap]
rs2245195	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs2245610	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318389	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2454195	0.85[ASN][1000 genomes]
rs2454196	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2454197	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487739	0.88[ASN][1000 genomes]
rs2487740	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2487746	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2504032	0.93[ASN][1000 genomes]
rs2504033	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2504034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs2504035	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504038	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504039	0.85[ASN][1000 genomes]
rs2504040	0.85[ASN][1000 genomes]
rs2504041	0.85[ASN][1000 genomes]
rs2504042	0.85[ASN][1000 genomes]
rs2504043	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504053	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs3845381	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3845382	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs3845383	0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs3856045	0.85[ASN][1000 genomes]
rs3909014	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs3909015	0.85[ASN][1000 genomes]
rs4469684	0.85[ASN][1000 genomes]
rs4511077	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4651050	0.82[ASN][1000 genomes]
rs60556788	0.83[ASN][1000 genomes]
rs61828370	0.84[ASN][1000 genomes]
rs6663482	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548339	chr1:179686244-179722827	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2245702	TNR	cis	parietal	SCAN
rs2245702	SH3BGRL2	trans	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179711400-179712000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
2	chr1:179711400-179714400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:179711600-179712000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
4	chr1:179711600-179712000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr1:179711600-179712000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:179711600-179712000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:179711600-179712000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:179711600-179712000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:179711600-179712000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr1:179711600-179712000	Bivalent Enhancer	Fetal Stomach	stomach
11	chr1:179711600-179712000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
12	chr1:179711600-179712400	Bivalent Enhancer	Fetal Brain Male	brain
13	chr1:179711600-179712400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
14	chr1:179711600-179712400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr1:179711600-179712400	Bivalent Enhancer	Stomach Mucosa	stomach
16	chr1:179711600-179713200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
17	chr1:179711600-179713200	Bivalent Enhancer	Fetal Lung	lung
18	chr1:179711600-179713400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:179711600-179713600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:179711600-179713800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr1:179711600-179713800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:179711600-179713800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr1:179711600-179714000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr1:179711600-179714000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr1:179711800-179712000	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:179711800-179712000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:179711800-179712000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:179711800-179712000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
29	chr1:179711800-179712000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr1:179711800-179712000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:179711800-179712000	Bivalent Enhancer	Adipose Nuclei	Adipose
32	chr1:179711800-179712000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
33	chr1:179711800-179712000	Bivalent Enhancer	Colonic Mucosa	Colon
34	chr1:179711800-179712000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
35	chr1:179711800-179712000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr1:179711800-179712000	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr1:179711800-179712000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr1:179711800-179712200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr1:179711800-179712200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:179711800-179712200	Bivalent Enhancer	Esophagus	oesophagus
41	chr1:179711800-179712200	Enhancers	Gastric	stomach
42	chr1:179711800-179712200	Bivalent Enhancer	Left Ventricle	heart
43	chr1:179711800-179712200	Enhancers	Pancreas	Pancrea
44	chr1:179711800-179712200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
45	chr1:179711800-179712200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
46	chr1:179711800-179712200	Bivalent Enhancer	NH-A	brain
47	chr1:179711800-179712200	Bivalent/Poised TSS	NHEK	skin
48	chr1:179711800-179712400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:179711800-179712400	Bivalent Enhancer	Primary T cells from cord blood	blood
50	chr1:179711800-179712400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood

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