Variant report

Variant	rs4653856
Chromosome Location	chr1:227753072-227753073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227749843..227751616-chr1:227752949..227754872,2	K562	blood:
2	chr1:227751959..227755569-chr1:227762720..227764448,3	MCF-7	breast:
3	chr1:227746809..227749278-chr1:227751802..227753794,2	K562	blood:
4	chr1:227751815..227753395-chr1:227758245..227760827,2	K562	blood:
5	chr1:227695645..227697944-chr1:227752053..227753592,2	K562	blood:

Variant related genes	Relation type
ENSG00000202264	Chromatin interaction
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1056699	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1060295	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs10799430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799439	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916188	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916191	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916203	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs1155807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12025942	1.00[CEU][hapmap];0.92[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];0.99[ASN][1000 genomes]
rs12033000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033610	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810680	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1923823	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2104245	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132368	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172937	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236360	0.91[CEU][hapmap];0.80[JPT][hapmap]
rs4500311	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426468	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426473	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6660432	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693054	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6703846	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7526184	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs7533588	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs7534403	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7536765	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539282	0.92[CEU][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227751800-227756400	Weak transcription	Spleen	Spleen
2	chr1:227752000-227753600	Weak transcription	Placenta	Placenta
3	chr1:227752000-227754000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227752000-227755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:227752000-227756200	Weak transcription	Gastric	stomach
6	chr1:227752000-227756400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:227752000-227756400	Weak transcription	Lung	lung
8	chr1:227752000-227757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227752000-227759800	Weak transcription	Left Ventricle	heart
10	chr1:227752000-227760000	Weak transcription	Esophagus	oesophagus
11	chr1:227752000-227766800	Weak transcription	Ovary	ovary
12	chr1:227752200-227753200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr1:227752200-227753200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:227752200-227753200	Enhancers	Psoas Muscle	Psoas
15	chr1:227752200-227753400	Enhancers	Thymus	Thymus
16	chr1:227752200-227754000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:227752200-227754200	Weak transcription	Brain Angular Gyrus	brain
18	chr1:227752200-227755000	Weak transcription	Colonic Mucosa	Colon
19	chr1:227752200-227755600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:227752200-227756200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:227752200-227756400	Weak transcription	Right Ventricle	heart
22	chr1:227752200-227758200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:227752200-227758800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:227752200-227760000	Weak transcription	Fetal Intestine Large	intestine
25	chr1:227752200-227763200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
27	chr1:227752400-227753200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:227752400-227753200	Enhancers	Fetal Brain Male	brain
29	chr1:227752400-227753200	Enhancers	Fetal Lung	lung
30	chr1:227752400-227753600	Weak transcription	A549	lung
31	chr1:227752400-227753600	Weak transcription	NH-A	brain
32	chr1:227752400-227753800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:227752400-227753800	Weak transcription	Fetal Intestine Small	intestine
34	chr1:227752400-227753800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:227752400-227754000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:227752400-227754000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:227752400-227754000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:227752400-227754000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:227752400-227754600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:227752400-227755000	Weak transcription	Fetal Thymus	thymus
41	chr1:227752400-227755000	Weak transcription	HepG2	liver
42	chr1:227752400-227755200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:227752400-227755400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:227752400-227755600	Weak transcription	HSMM	muscle
45	chr1:227752400-227755800	Weak transcription	NHLF	lung
46	chr1:227752400-227756000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:227752400-227756200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:227752400-227756600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:227752400-227756600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:227752400-227757000	Weak transcription	NHDF-Ad	bronchial

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