Variant report

Variant	rs10804183
Chromosome Location	chr2:211327901-211327902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10195342	0.85[EUR][1000 genomes]
rs1027901	0.81[EUR][1000 genomes]
rs1044708	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10490318	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs10804182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804185	0.81[CHB][hapmap]
rs11690895	0.87[ASN][1000 genomes]
rs11889228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11894867	0.82[EUR][1000 genomes]
rs11896108	0.82[EUR][1000 genomes]
rs11900468	0.82[EUR][1000 genomes]
rs12466705	0.81[CHB][hapmap]
rs12469589	0.82[EUR][1000 genomes]
rs12473150	0.80[EUR][1000 genomes]
rs12474078	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs12477237	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12611623	0.81[CHB][hapmap]
rs1350463	0.82[EUR][1000 genomes]
rs16844534	0.81[CHB][hapmap]
rs17771664	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs17772042	0.80[CHB][hapmap]
rs17822981	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1812875	0.83[EUR][1000 genomes]
rs2042049	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs2287424	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287425	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287430	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2287432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287433	0.88[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2370949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2370956	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2887899	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35314871	0.80[EUR][1000 genomes]
rs3732055	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs3755184	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770689	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770694	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770695	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770699	0.88[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821136	0.81[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs3845633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4372818	0.81[CHB][hapmap]
rs4467201	0.85[EUR][1000 genomes]
rs4609985	0.81[EUR][1000 genomes]
rs4673526	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4673528	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4673529	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6435569	0.85[EUR][1000 genomes]
rs6711129	0.81[CHB][hapmap]
rs6717228	0.80[EUR][1000 genomes]
rs6725303	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6725770	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6727182	0.84[ASN][1000 genomes]
rs6729280	0.81[CHB][hapmap]
rs6752320	0.81[CHB][hapmap]
rs6756422	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72930503	0.98[ASN][1000 genomes]
rs72930539	0.92[ASN][1000 genomes]
rs7578688	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595022	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10804183	CPS1	cis	parietal	SCAN
rs10804183	CPS1	cis	cerebellum	SCAN
rs10804183	LANCL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
5	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
6	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
7	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:211299800-211330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:211300400-211329800	Weak transcription	A549	lung
11	chr2:211301200-211330000	Weak transcription	Gastric	stomach
12	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
14	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:211301400-211330000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:211301400-211330800	Weak transcription	Right Ventricle	heart
17	chr2:211301400-211334400	Weak transcription	NHEK	skin
18	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:211306000-211330000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:211308000-211332400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:211314200-211328800	Strong transcription	Primary T cells from cord blood	blood
22	chr2:211315400-211340000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:211315600-211337800	Strong transcription	Fetal Thymus	thymus
24	chr2:211315600-211339600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:211315800-211337200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:211315800-211337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:211316000-211338000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:211316200-211337800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:211316200-211337800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:211316600-211339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:211316800-211338800	Strong transcription	Dnd41	blood
32	chr2:211318000-211337800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:211319600-211330000	Weak transcription	NH-A	brain
34	chr2:211320000-211330200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:211320000-211331000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:211320000-211331200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:211320000-211333200	Weak transcription	NHLF	lung
38	chr2:211320400-211329800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:211321000-211329400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:211321000-211331400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:211321000-211334200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:211321200-211337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:211322400-211340400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:211322600-211340400	Weak transcription	K562	blood
45	chr2:211322800-211329800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:211323200-211328600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:211323200-211329800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:211323200-211330800	Weak transcription	Spleen	Spleen
49	chr2:211323200-211330800	Weak transcription	Osteobl	bone
50	chr2:211323200-211333200	Weak transcription	Pancreas	Pancrea

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