Variant report

Variant	rs1558854
Chromosome Location	chr2:39639572-39639573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39635276..39640508-chr2:39640941..39645614,10	K562	blood:
2	chr2:39637044..39640702-chr2:39646028..39648764,3	K562	blood:
3	chr2:39638402..39640508-chr2:39641916..39643907,2	K562	blood:
4	chr2:39625232..39628414-chr2:39637317..39639794,4	K562	blood:
5	chr2:39624807..39627071-chr2:39638065..39639781,2	MCF-7	breast:
6	chr2:39635451..39641229-chr2:39641645..39645299,6	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10175094	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs10185961	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs10865148	0.82[JPT][hapmap]
rs11124671	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs11124680	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11677383	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12151392	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs12328727	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12617901	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs12712634	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12712640	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1861733	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs1861734	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs2024514	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3755171	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3755176	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs3770662	0.94[JPT][hapmap]
rs3770664	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs3770671	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3770672	0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3887311	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544214	0.86[CHB][hapmap]
rs6544221	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709424	0.86[CHB][hapmap]
rs6714566	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7573923	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7598583	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7603337	0.83[ASN][1000 genomes]
rs9037	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs9309036	0.84[CEU][hapmap]
rs9309037	0.86[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:39622600-39643600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:39622800-39643200	Weak transcription	Fetal Brain Male	brain
4	chr2:39622800-39643400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:39627400-39639600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:39630800-39640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39632400-39643400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:39632600-39640400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:39632600-39641400	Enhancers	Fetal Heart	heart
10	chr2:39632800-39639600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:39633000-39640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39633000-39641200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:39633000-39644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:39634400-39641000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:39634600-39643800	Weak transcription	Fetal Brain Female	brain
16	chr2:39635000-39640400	Weak transcription	Pancreas	Pancrea
17	chr2:39635000-39644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:39635400-39643200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:39635600-39640200	Weak transcription	Liver	Liver
20	chr2:39635600-39640400	Weak transcription	Gastric	stomach
21	chr2:39635600-39643400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:39636200-39642400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:39636600-39640400	Enhancers	HSMMtube	muscle
24	chr2:39636600-39640600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:39636600-39651400	Weak transcription	Fetal Thymus	thymus
26	chr2:39636800-39639800	Enhancers	NHEK	skin
27	chr2:39636800-39640400	Weak transcription	Spleen	Spleen
28	chr2:39636800-39641000	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr2:39636800-39641600	Enhancers	Colon Smooth Muscle	Colon
30	chr2:39637000-39639600	Enhancers	Fetal Lung	lung
31	chr2:39637200-39647000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:39637400-39640400	Weak transcription	Fetal Intestine Large	intestine
34	chr2:39637600-39640600	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:39637600-39643800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:39637600-39651400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:39638000-39640600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:39638200-39639600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:39638200-39639800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:39638200-39639800	Enhancers	Small Intestine	intestine
41	chr2:39638200-39641000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:39638200-39641000	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:39638200-39641400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr2:39638200-39641400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:39638200-39641400	Enhancers	Brain Anterior Caudate	brain
46	chr2:39638400-39639600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:39638400-39639600	Genic enhancers	HepG2	liver
48	chr2:39638400-39639800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:39638400-39639800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr2:39638400-39639800	Enhancers	Skeletal Muscle Female	skeletal muscle

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