Variant report

Variant	rs2292931
Chromosome Location	chr2:7137488-7137489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495549	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10929458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11898648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465410	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393491	1.00[JPT][hapmap]
rs13398488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13399190	1.00[JPT][hapmap]
rs13418719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13422407	0.93[ASN][1000 genomes]
rs1797554	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2460404	0.85[AFR][1000 genomes]
rs2460405	0.81[YRI][hapmap]
rs28768765	0.85[ASN][1000 genomes]
rs309314	0.81[AFR][1000 genomes]
rs309317	0.86[AFR][1000 genomes]
rs309319	0.86[AFR][1000 genomes]
rs309322	0.87[AFR][1000 genomes]
rs3755509	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs414941	0.88[AFR][1000 genomes]
rs443852	0.91[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs447721	0.91[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs4669124	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4669126	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6741819	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs700943	0.83[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72781779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs771253	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs771256	0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[ASN][1000 genomes]
rs771257	1.00[JPT][hapmap]
rs771259	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs771263	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs771265	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs771266	0.83[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][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	nsv833326	chr2:6985027-7142564	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv978975	chr2:7136211-7137757	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292931	RNF144A	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
2	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:7115800-7148800	Weak transcription	Esophagus	oesophagus
4	chr2:7121200-7145400	Weak transcription	Thymus	Thymus
5	chr2:7121400-7148200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:7124000-7157600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:7126600-7147600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:7126800-7141800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:7126800-7148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:7127200-7154000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:7127600-7138800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:7127600-7143600	Weak transcription	HepG2	liver
13	chr2:7131000-7167600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:7131200-7141000	Strong transcription	Primary T cells from cord blood	blood
15	chr2:7131200-7146800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:7131400-7150200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:7131400-7162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:7131600-7154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:7131600-7154200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:7131800-7139000	Weak transcription	Fetal Thymus	thymus
21	chr2:7132800-7146600	Weak transcription	Fetal Heart	heart
22	chr2:7133400-7147400	Weak transcription	Fetal Kidney	kidney
23	chr2:7133800-7138600	Weak transcription	Ovary	ovary
24	chr2:7133800-7147400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:7133800-7147600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:7133800-7147800	Weak transcription	Fetal Brain Female	brain
27	chr2:7133800-7150800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:7134400-7140800	Strong transcription	Dnd41	blood
29	chr2:7134400-7147400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:7134600-7139000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:7134600-7139200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:7135000-7138600	Weak transcription	Right Ventricle	heart
33	chr2:7135000-7138800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:7135000-7139000	Weak transcription	Primary B cells from cord blood	blood
35	chr2:7135000-7139200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:7135000-7146800	Weak transcription	Lung	lung
37	chr2:7135200-7138000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:7135200-7138400	Weak transcription	Fetal Lung	lung
39	chr2:7135200-7138400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:7135200-7138600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:7135200-7138600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr2:7135200-7139000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:7135200-7145400	Weak transcription	Fetal Brain Male	brain
44	chr2:7135400-7137800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:7135400-7138600	Weak transcription	Pancreas	Pancrea
46	chr2:7135400-7139400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:7135400-7139400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:7135400-7145000	Weak transcription	Brain Germinal Matrix	brain
49	chr2:7135600-7139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:7135800-7138800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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