Variant report

Variant	rs1504136
Chromosome Location	chr2:127977118-127977119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127957550..127959520-chr2:127975505..127977152,2	MCF-7	breast:
2	chr2:127975205..127977314-chr2:127992465..127995136,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11890243	0.82[CEU][hapmap]
rs13017099	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13385611	0.88[CHB][hapmap]
rs13429050	0.88[CHB][hapmap]
rs13431911	0.88[CHB][hapmap]
rs1604817	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2404532	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4536600	1.00[CHB][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs4662714	0.83[EUR][1000 genomes]
rs4662715	0.81[EUR][1000 genomes]
rs6430934	0.93[EUR][1000 genomes]
rs6710496	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567389	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585314	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv961678	chr2:127961305-127979990	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3331416	chr2:127962771-127980988	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1504136	MAP3K2	cis	cerebellum	SCAN
rs1504136	ERCC3	cis	Adipose Subcutaneous	GTEx
rs1504136	ERCC3	cis	parietal	SCAN
rs1504136	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127975200-127977200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:127975600-127977200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:127975600-127977800	Enhancers	Lung	lung
4	chr2:127975600-127978200	Active TSS	NHEK	skin
5	chr2:127975600-127979000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:127975800-127977200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr2:127975800-127978000	Active TSS	Esophagus	oesophagus
8	chr2:127975800-127978200	Active TSS	A549	lung
9	chr2:127975800-127978800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:127976000-127977200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
11	chr2:127976000-127977800	Active TSS	NH-A	brain
12	chr2:127976000-127978800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:127976200-127977200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
14	chr2:127976200-127977200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:127976200-127977200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
16	chr2:127976200-127977200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
17	chr2:127976200-127977400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:127976200-127977400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
19	chr2:127976200-127977400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:127976200-127977400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr2:127976200-127977400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr2:127976200-127977400	Flanking Bivalent TSS/Enh	Osteobl	bone
23	chr2:127976200-127977600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
24	chr2:127976200-127977600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:127976200-127977600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:127976200-127977600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:127976200-127977600	Bivalent/Poised TSS	Fetal Stomach	stomach
28	chr2:127976200-127978000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:127976200-127978000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
30	chr2:127976200-127978000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:127976200-127978000	Active TSS	Fetal Lung	lung
32	chr2:127976200-127978200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:127976200-127978200	Active TSS	Fetal Kidney	kidney
34	chr2:127976200-127978400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:127976200-127978400	Active TSS	Brain Substantia Nigra	brain
36	chr2:127976200-127978600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
37	chr2:127976200-127978800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr2:127976200-127979000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr2:127976400-127977200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
41	chr2:127976400-127977200	Flanking Active TSS	Liver	Liver
42	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
43	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr2:127976400-127977200	Bivalent Enhancer	Fetal Heart	heart
45	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
46	chr2:127976400-127977200	Active TSS	Gastric	stomach
47	chr2:127976400-127977200	Flanking Active TSS	Ovary	ovary
48	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
49	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
50	chr2:127976400-127977200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

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