Variant report

Variant	rs1354904
Chromosome Location	chr2:189441749-189441750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189439657..189442123-chr2:189444360..189445883,2	K562	blood:
2	chr2:189436897..189438874-chr2:189440329..189441944,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10199260	1.00[JPT][hapmap]
rs10804021	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10931363	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10931369	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931376	0.85[EUR][1000 genomes]
rs11676859	0.85[EUR][1000 genomes]
rs11683089	0.95[EUR][1000 genomes]
rs11683183	0.95[EUR][1000 genomes]
rs11686702	0.81[EUR][1000 genomes]
rs11695316	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11889220	0.90[EUR][1000 genomes]
rs11889402	0.81[EUR][1000 genomes]
rs12463744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475894	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12476413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12988921	0.89[EUR][1000 genomes]
rs13011602	0.85[EUR][1000 genomes]
rs13012993	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13025659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13386581	0.94[ASN][1000 genomes]
rs13386959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13392850	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13393057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13396968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13397653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13412448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13413644	0.94[ASN][1000 genomes]
rs13413752	0.94[ASN][1000 genomes]
rs13414327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13418031	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13424809	0.83[ASN][1000 genomes]
rs1354902	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1354905	0.84[YRI][hapmap]
rs1354906	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1354908	0.94[EUR][1000 genomes]
rs1354910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1395868	0.85[EUR][1000 genomes]
rs1507551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1507560	0.93[EUR][1000 genomes]
rs1507561	0.94[EUR][1000 genomes]
rs1567184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580993	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1605462	0.90[YRI][hapmap]
rs1911602	0.87[EUR][1000 genomes]
rs1911603	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2350903	0.93[EUR][1000 genomes]
rs2882532	0.81[EUR][1000 genomes]
rs3935690	0.82[EUR][1000 genomes]
rs4146570	0.93[EUR][1000 genomes]
rs4146571	0.81[EUR][1000 genomes]
rs4453658	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4591284	0.91[EUR][1000 genomes]
rs4667229	1.00[JPT][hapmap]
rs4667231	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61045757	1.00[ASN][1000 genomes]
rs66641143	1.00[ASN][1000 genomes]
rs6707212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6708451	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6709557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6727633	0.89[ASN][1000 genomes]
rs67425558	0.89[ASN][1000 genomes]
rs6744275	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6756504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7419798	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7420808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7422739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7423554	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7568147	0.89[ASN][1000 genomes]
rs7582643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7587596	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7596299	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs955813	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv533110	chr2:189354436-189462552	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189384800-189442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:189414600-189453600	Weak transcription	HUVEC	blood vessel
3	chr2:189417000-189445600	Weak transcription	NHLF	lung
4	chr2:189420200-189454800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:189420600-189463200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:189421400-189450000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:189422800-189448800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:189423000-189449800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:189424200-189449800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:189426000-189449800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:189426600-189456200	Weak transcription	Gastric	stomach
12	chr2:189426800-189445800	Weak transcription	Fetal Stomach	stomach
13	chr2:189427000-189449000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:189427200-189445600	Weak transcription	Aorta	Aorta
15	chr2:189431400-189463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:189433600-189456000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:189433600-189459400	Weak transcription	Psoas Muscle	Psoas
18	chr2:189434400-189445800	Weak transcription	Adipose Nuclei	Adipose
19	chr2:189434400-189463200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:189434400-189465000	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:189435800-189448800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:189436400-189463200	Weak transcription	Ovary	ovary
23	chr2:189436600-189449600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:189436600-189449600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:189436800-189446000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:189436800-189448800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:189437000-189443000	Weak transcription	Placenta	Placenta
28	chr2:189437000-189448600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:189437000-189449000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:189437000-189454400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:189438400-189448800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:189439000-189449800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:189439200-189448800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:189439400-189449800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:189439400-189449800	Weak transcription	Pancreas	Pancrea
36	chr2:189440000-189448800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:189440200-189449600	Weak transcription	Fetal Lung	lung
38	chr2:189440400-189442600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:189440600-189452400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:189441200-189441800	Enhancers	Osteobl	bone
41	chr2:189441200-189442400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr2:189441200-189442800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:189441400-189442000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:189441400-189442000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:189441400-189442200	Enhancers	Colon Smooth Muscle	Colon
46	chr2:189441600-189442000	Enhancers	Stomach Smooth Muscle	stomach
47	chr2:189441600-189442200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:189441600-189442200	Flanking Active TSS	NHDF-Ad	bronchial

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