Variant report

Variant	rs3844054
Chromosome Location	chr1:62752542-62752543
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	chr1:62750494..62753386-chr1:62754498..62756263,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10889317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207949	0.86[EUR][1000 genomes]
rs12037540	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044289	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12064402	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12082623	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12095092	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12095173	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1325742	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666483	0.86[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs2666501	0.87[EUR][1000 genomes]
rs2666502	0.90[EUR][1000 genomes]
rs2765265	0.83[CEU][hapmap]
rs2765267	0.83[CEU][hapmap]
rs3844053	0.81[EUR][1000 genomes]
rs3850631	0.91[EUR][1000 genomes]
rs3895339	0.82[EUR][1000 genomes]
rs4915609	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4915811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915812	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4915813	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4915814	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4915815	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587965	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663943	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs7551135	0.91[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62749000-62753000	Enhancers	Fetal Lung	lung
2	chr1:62750800-62753200	Enhancers	HMEC	breast
3	chr1:62751000-62752600	Bivalent Enhancer	Fetal Intestine Large	intestine
4	chr1:62751000-62753000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:62751200-62753400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:62751400-62752600	Enhancers	A549	lung
7	chr1:62751400-62752800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:62751400-62753200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr1:62751600-62752600	Enhancers	Liver	Liver
10	chr1:62751600-62752600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
11	chr1:62751600-62752800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
12	chr1:62751600-62752800	Bivalent Enhancer	Fetal Brain Male	brain
13	chr1:62751600-62753000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
14	chr1:62751600-62753000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr1:62751600-62753000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
16	chr1:62751600-62753000	Bivalent Enhancer	Fetal Stomach	stomach
17	chr1:62751600-62753200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:62751600-62753200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:62751600-62753200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr1:62751600-62753200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:62751600-62753400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr1:62751600-62754200	Enhancers	Placenta	Placenta
23	chr1:62751600-62754800	Enhancers	Fetal Heart	heart
24	chr1:62751600-62755000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:62751600-62756200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:62751800-62752600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:62751800-62752600	Enhancers	Fetal Intestine Small	intestine
28	chr1:62751800-62752600	Bivalent Enhancer	Fetal Thymus	thymus
29	chr1:62751800-62752600	Enhancers	Ovary	ovary
30	chr1:62751800-62752800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:62751800-62753000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
32	chr1:62751800-62753000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:62751800-62753000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:62751800-62753000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:62751800-62753000	Flanking Active TSS	HepG2	liver
36	chr1:62751800-62753200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:62751800-62754800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:62752000-62752600	Enhancers	Brain Angular Gyrus	brain
39	chr1:62752000-62752600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
40	chr1:62752000-62752800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
41	chr1:62752000-62752800	Bivalent Enhancer	Stomach Mucosa	stomach
42	chr1:62752000-62752800	Bivalent Enhancer	HUVEC	blood vessel
43	chr1:62752000-62753200	Bivalent Enhancer	Esophagus	oesophagus
44	chr1:62752000-62753200	Enhancers	Fetal Muscle Trunk	muscle
45	chr1:62752000-62753200	Enhancers	Pancreas	Pancrea
46	chr1:62752000-62753200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:62752000-62753400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:62752200-62752600	Weak transcription	Gastric	stomach
49	chr1:62752200-62752600	Weak transcription	Right Atrium	heart
50	chr1:62752200-62752600	Flanking Active TSS	Hela-S3	cervix

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