Variant report

Variant	rs3754944
Chromosome Location	chr2:231279616-231279617
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:231279532-231281659	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:231279555-231281531	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:231279589-231281563	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:231279542-231281558	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10180055	0.92[ASN][1000 genomes]
rs10180131	0.91[ASN][1000 genomes]
rs10191049	0.87[ASN][1000 genomes]
rs10207311	0.93[ASN][1000 genomes]
rs10804365	0.87[ASN][1000 genomes]
rs11682084	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11688912	0.89[ASN][1000 genomes]
rs11689240	0.91[ASN][1000 genomes]
rs11690286	0.91[ASN][1000 genomes]
rs11898168	0.96[ASN][1000 genomes]
rs12694847	0.81[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs12694861	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12694865	0.88[GIH][hapmap]
rs13411346	0.92[ASN][1000 genomes]
rs13411566	0.93[ASN][1000 genomes]
rs3754940	0.86[GIH][hapmap]
rs3754942	0.86[GIH][hapmap]
rs4142872	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs56102622	0.90[ASN][1000 genomes]
rs56377716	0.88[ASN][1000 genomes]
rs62193378	0.92[ASN][1000 genomes]
rs62193388	0.90[ASN][1000 genomes]
rs6436937	0.96[ASN][1000 genomes]
rs6722012	0.96[ASN][1000 genomes]
rs6730329	0.92[ASN][1000 genomes]
rs6748062	0.93[ASN][1000 genomes]
rs6748069	0.93[ASN][1000 genomes]
rs6756448	0.95[ASN][1000 genomes]
rs7581828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7582700	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7595408	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs973504	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3754944	EIF4E2	cis	parietal	SCAN
rs3754944	NMUR1	cis	parietal	SCAN
rs3754944	SP140L	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231277200-231280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:231277200-231280400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:231277200-231280400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:231277200-231280400	Weak transcription	Aorta	Aorta
5	chr2:231277200-231280400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:231277200-231280400	Weak transcription	Psoas Muscle	Psoas
7	chr2:231277200-231280400	Weak transcription	Small Intestine	intestine
8	chr2:231277200-231280400	Weak transcription	HSMM	muscle
9	chr2:231277200-231280400	Weak transcription	HSMMtube	muscle
10	chr2:231277200-231280400	Weak transcription	NH-A	brain
11	chr2:231277200-231280800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:231277400-231279800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:231277400-231279800	Weak transcription	Osteobl	bone
14	chr2:231277400-231280000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:231277400-231280000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:231277400-231280200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:231277400-231280200	Enhancers	Primary T cells from cord blood	blood
18	chr2:231277400-231280200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:231277400-231280200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:231277400-231280200	Weak transcription	HUVEC	blood vessel
21	chr2:231277400-231280400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr2:231277400-231280400	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:231277400-231280400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr2:231277400-231280400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:231277400-231280400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:231277400-231280400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:231277400-231280400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:231277400-231280400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:231277400-231280400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:231277400-231280400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:231277400-231280400	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:231277400-231280400	Weak transcription	Fetal Lung	lung
33	chr2:231277400-231280400	Weak transcription	A549	lung
34	chr2:231277400-231280400	Enhancers	HepG2	liver
35	chr2:231277400-231280600	Weak transcription	Fetal Brain Male	brain
36	chr2:231277400-231280600	Weak transcription	Fetal Kidney	kidney
37	chr2:231277600-231279800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:231277600-231279800	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:231277600-231279800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:231277600-231279800	Weak transcription	Pancreas	Pancrea
41	chr2:231277600-231280000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:231277600-231280000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:231277600-231280200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:231277600-231280200	Weak transcription	Adipose Nuclei	Adipose
45	chr2:231277600-231280200	Weak transcription	Fetal Intestine Large	intestine
46	chr2:231277600-231280400	Enhancers	Primary B cells from cord blood	blood
47	chr2:231277600-231280400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:231277600-231280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:231277600-231280400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:231277600-231280400	Weak transcription	Thymus	Thymus

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