Variant report

Variant	rs700943
Chromosome Location	chr2:7126569-7126570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10495548	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]
rs10495549	0.83[CEU][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10929458	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11898648	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12465410	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13393491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13398488	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13399190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13408347	0.94[ASN][1000 genomes]
rs13418719	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13422407	0.87[ASN][1000 genomes]
rs1797554	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292931	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]
rs28768765	0.84[ASN][1000 genomes]
rs3755509	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4669124	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6741819	0.83[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72781779	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs771253	0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs771256	0.81[ASW][hapmap];0.83[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs771257	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs771259	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs771263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs771265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs771266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs932196	0.87[CEU][hapmap]

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	nsv2598	chr2:7088737-7133415	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs700943	ODC1	cis	parietal	SCAN
rs700943	RNF144A	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7083800-7129600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:7101000-7130000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
4	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:7109200-7137000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:7115800-7148800	Weak transcription	Esophagus	oesophagus
7	chr2:7119200-7126800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:7121200-7130800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:7121200-7145400	Weak transcription	Thymus	Thymus
10	chr2:7121400-7129400	Weak transcription	Fetal Thymus	thymus
11	chr2:7121400-7148200	Weak transcription	Fetal Intestine Small	intestine
12	chr2:7121800-7130200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:7122000-7128000	Enhancers	Pancreas	Pancrea
14	chr2:7122600-7126800	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:7123600-7127000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:7123600-7133400	Weak transcription	Fetal Stomach	stomach
17	chr2:7123800-7131000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:7123800-7132400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:7124000-7126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:7124000-7130800	Weak transcription	Fetal Brain Female	brain
21	chr2:7124000-7132000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:7124000-7132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:7124000-7157600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:7124200-7126600	Weak transcription	Ovary	ovary
25	chr2:7124200-7129600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:7124600-7126600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:7124800-7127000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:7124800-7127200	Enhancers	Brain Angular Gyrus	brain
29	chr2:7125000-7127200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:7125000-7128000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:7125200-7127800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:7125400-7127600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:7125400-7127800	Enhancers	Spleen	Spleen
34	chr2:7125600-7126600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:7125600-7126800	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:7125600-7127800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:7126000-7127600	Enhancers	Fetal Brain Male	brain
38	chr2:7126000-7127800	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:7126000-7127800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:7126000-7127800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr2:7126000-7128000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:7126000-7128000	Enhancers	Brain Germinal Matrix	brain
43	chr2:7126000-7128000	Enhancers	Fetal Muscle Leg	muscle
44	chr2:7126000-7128000	Enhancers	Left Ventricle	heart
45	chr2:7126000-7128400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:7126200-7126600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:7126200-7126600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:7126200-7126600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr2:7126200-7126600	Enhancers	Stomach Mucosa	stomach
50	chr2:7126200-7126800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links