Variant report

Variant	rs2297649
Chromosome Location	chr1:155935244-155935245
allele	A/C
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	POLR2A	chr1:155934766-155935513	HL-60	blood:	n/a	n/a
2	POLR2A	chr1:155934091-155936451	U87	brain:	n/a	n/a
3	POLR2A	chr1:155934721-155935289	K562	blood:	n/a	n/a
4	POLR2A	chr1:155934554-155936451	U87	brain:	n/a	n/a
5	POLR2A	chr1:155934796-155935347	U87	brain:	n/a	n/a

Variant related genes	Relation type
ARHGEF2	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10796955	0.95[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10908483	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1111102	0.81[CEU][hapmap]
rs11264426	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585845	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026057	0.84[AMR][1000 genomes]
rs12037177	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12080846	0.95[ASN][1000 genomes]
rs12091273	0.95[ASN][1000 genomes]
rs12091361	0.95[ASN][1000 genomes]
rs12118795	0.86[CEU][hapmap];0.87[TSI][hapmap]
rs12144175	0.81[AMR][1000 genomes]
rs12568523	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1889532	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1889533	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2016251	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282301	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2364403	0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs3820594	0.91[MEX][hapmap]
rs4661217	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4661218	0.95[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61813286	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6427297	0.81[TSI][hapmap]
rs66466805	0.82[AMR][1000 genomes]
rs6667652	1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs6670477	0.80[AMR][1000 genomes]
rs6670493	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6696019	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs72708205	0.81[AMR][1000 genomes]
rs7534858	0.95[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545308	0.80[AMR][1000 genomes]
rs867548	0.82[AMR][1000 genomes]
rs867549	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs867550	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs915178	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs915181	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs928596	0.95[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2297649	RIT1	cis	Thyroid	GTEx
rs2297649	SPRR3	cis	parietal	SCAN
rs2297649	YY1AP1	cis	cerebellum	SCAN
rs2297649	RIT1	cis	cerebellum	SCAN
rs2297649	ROBLD3	cis	parietal	SCAN
rs2297649	HAPLN2	cis	parietal	SCAN
rs2297649	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2297649	ADAM15	cis	multi-tissue	Pritchard
rs2297649	PRUNE	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155911200-155940000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155915200-155936800	Strong transcription	Fetal Brain Female	brain
4	chr1:155915200-155937000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155915800-155936600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:155916000-155937000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155916200-155937000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:155916400-155936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:155916400-155936400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:155916400-155936600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:155916400-155937200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:155916400-155937400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:155916600-155935800	Strong transcription	Fetal Intestine Small	intestine
14	chr1:155916600-155937000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:155916600-155937200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:155916800-155937000	Strong transcription	Thymus	Thymus
17	chr1:155917000-155937200	Strong transcription	Fetal Intestine Large	intestine
18	chr1:155917000-155939400	Strong transcription	Dnd41	blood
19	chr1:155917200-155936800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:155917600-155936400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:155917600-155937000	Strong transcription	Fetal Thymus	thymus
22	chr1:155917800-155936400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:155918000-155936000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:155918000-155936000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:155919600-155936400	Strong transcription	Primary T cells from cord blood	blood
26	chr1:155924000-155937200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:155926400-155937200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:155926800-155936400	Strong transcription	Fetal Lung	lung
29	chr1:155926800-155937200	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr1:155926800-155937200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:155928200-155936600	Weak transcription	Fetal Brain Male	brain
32	chr1:155929400-155935800	Strong transcription	HepG2	liver
33	chr1:155929600-155936200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:155929600-155936400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr1:155929800-155937400	Strong transcription	Pancreas	Pancrea
36	chr1:155930800-155939400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:155931000-155940000	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr1:155932000-155936000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:155932000-155936200	Strong transcription	Fetal Kidney	kidney
40	chr1:155932800-155936800	Strong transcription	Colon Smooth Muscle	Colon
41	chr1:155932800-155936800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:155932800-155937200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:155932800-155938800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:155932800-155939600	Strong transcription	Osteobl	bone
45	chr1:155933000-155935400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:155933000-155935400	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:155933000-155935400	Strong transcription	Placenta	Placenta
48	chr1:155933000-155935800	Weak transcription	Small Intestine	intestine
49	chr1:155933000-155936200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:155933000-155936200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links