Variant report

Variant	rs3754595
Chromosome Location	chr2:234370425-234370426
allele	A/G
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	chr2:234370185-234370713	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:234370167-234370788	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:234369738-234372020	A549	lung:	n/a	n/a
4	POLR2A	chr2:234370423-234370441	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:234369640-234373471	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:234370282-234371464	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234368228..234370578-chr2:234375151..234377494,2	MCF-7	breast:
2	chr2:234368802..234371740-chr2:234380703..234384400,4	MCF-7	breast:

Variant related genes	Relation type
DGKD	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1046976	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10929178	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11675254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11675858	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11676524	1.00[CHB][hapmap]
rs11681704	0.85[EUR][1000 genomes]
rs11686188	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11694406	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2228939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768799	0.96[EUR][1000 genomes]
rs3768801	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768802	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796090	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs3796092	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3820744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828307	1.00[CHB][hapmap]
rs56266844	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56277462	0.93[EUR][1000 genomes]
rs56336977	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6704644	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap]
rs6746234	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6750618	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs72980338	0.87[EUR][1000 genomes]
rs72980361	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72980376	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72980392	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7597465	0.85[EUR][1000 genomes]
rs7598771	0.92[CEU][hapmap];1.00[CHB][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3754595	L1TD1	trans	lymphoblastoid	seeQTL
rs3754595	ECEL1P2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234322400-234371800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:234339600-234394200	Weak transcription	HUVEC	blood vessel
3	chr2:234339800-234391400	Weak transcription	NHDF-Ad	bronchial
4	chr2:234343000-234393000	Strong transcription	Primary T cells from cord blood	blood
5	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:234343200-234383000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:234344000-234382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:234344200-234382000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:234344200-234382200	Strong transcription	Primary B cells from cord blood	blood
10	chr2:234344200-234382600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:234344400-234381600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:234346600-234375000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:234348000-234370800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:234350200-234377600	Strong transcription	Left Ventricle	heart
15	chr2:234350400-234374400	Strong transcription	Fetal Intestine Large	intestine
16	chr2:234352400-234380800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:234352400-234382000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:234352600-234373600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:234352600-234380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:234352600-234380800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:234352600-234381400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:234352600-234381600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:234352600-234381800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:234352600-234382600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:234352600-234382600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:234352800-234382000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:234353000-234378000	Strong transcription	Rectal Smooth Muscle	rectum
28	chr2:234353400-234373600	Strong transcription	Aorta	Aorta
29	chr2:234353400-234379600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:234353400-234381600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:234353600-234373800	Strong transcription	Dnd41	blood
32	chr2:234353600-234381800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:234353800-234372600	Strong transcription	Placenta	Placenta
34	chr2:234353800-234378000	Strong transcription	Fetal Stomach	stomach
35	chr2:234354000-234373800	Strong transcription	Fetal Brain Female	brain
36	chr2:234354000-234377800	Weak transcription	Fetal Heart	heart
37	chr2:234354000-234381600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:234354200-234373400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:234355000-234377800	Strong transcription	Adipose Nuclei	Adipose
40	chr2:234356400-234374200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:234357600-234372600	Strong transcription	Esophagus	oesophagus
42	chr2:234357600-234382000	Strong transcription	Liver	Liver
43	chr2:234358000-234374200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:234358200-234372200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:234358200-234373200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:234358200-234378400	Strong transcription	Fetal Intestine Small	intestine
47	chr2:234358200-234379000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:234358200-234379400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:234358400-234372800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr2:234359400-234373800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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