Variant report

Variant	rs13406655
Chromosome Location	chr2:234345406-234345407
allele	G/T
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	chr2:234341455-234348135	A549	lung:	n/a	n/a
2	POLR2A	chr2:234344271-234346815	GM18505	blood:	n/a	n/a

Variant related genes	Relation type
DGKD	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10169180	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10178357	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10183033	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10185923	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10803653	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10929195	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1097930	0.82[JPT][hapmap]
rs1097931	0.82[ASN][1000 genomes]
rs11888993	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11897617	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1220430	0.82[JPT][hapmap]
rs12473824	1.00[CHB][hapmap]
rs12615446	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13391864	1.00[JPT][hapmap]
rs13392183	0.81[EUR][1000 genomes]
rs13393578	0.94[EUR][1000 genomes]
rs13400471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13403169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13406462	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13414407	0.82[JPT][hapmap]
rs13425849	0.82[JPT][hapmap]
rs1453321	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1470864	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1545525	0.82[JPT][hapmap]
rs1597940	0.82[JPT][hapmap]
rs2167884	0.82[JPT][hapmap]
rs2167885	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2305541	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2602387	0.82[CHB][hapmap]
rs2602389	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2603545	0.82[JPT][hapmap]
rs2603547	0.84[ASN][1000 genomes]
rs2924811	0.85[ASN][1000 genomes]
rs2971862	0.85[ASN][1000 genomes]
rs2971863	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2971864	0.85[ASN][1000 genomes]
rs2971867	0.85[ASN][1000 genomes]
rs59458664	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6710645	0.82[JPT][hapmap]
rs6713866	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6753062	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6756068	0.82[JPT][hapmap]
rs73117551	0.94[EUR][1000 genomes]
rs7571288	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7572257	1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7578898	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs838543	0.82[JPT][hapmap]
rs838544	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs838549	0.82[JPT][hapmap]
rs838550	0.82[JPT][hapmap]
rs838551	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs838552	0.82[JPT][hapmap]
rs838555	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs838559	0.84[ASN][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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:122 , 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	chr2:234329000-234351600	Weak transcription	Fetal Brain Male	brain
3	chr2:234329400-234346000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:234333400-234345600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:234335200-234357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:234338000-234358000	Weak transcription	NH-A	brain
7	chr2:234338400-234362800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:234338800-234360800	Weak transcription	HMEC	breast
9	chr2:234339200-234345600	Weak transcription	NHLF	lung
10	chr2:234339200-234346000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:234339200-234360000	Weak transcription	K562	blood
12	chr2:234339600-234346000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:234339600-234354800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:234339600-234394200	Weak transcription	HUVEC	blood vessel
15	chr2:234339800-234347800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:234339800-234347800	Weak transcription	Osteobl	bone
17	chr2:234339800-234391400	Weak transcription	NHDF-Ad	bronchial
18	chr2:234341600-234357400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:234341800-234354800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:234342600-234346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:234342800-234346000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:234342800-234351600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:234342800-234354800	Weak transcription	Fetal Kidney	kidney
24	chr2:234342800-234358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:234343000-234346400	Strong transcription	Fetal Muscle Leg	muscle
26	chr2:234343000-234346800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:234343000-234346800	Strong transcription	Brain Substantia Nigra	brain
28	chr2:234343000-234347800	Strong transcription	Adipose Nuclei	Adipose
29	chr2:234343000-234349200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:234343000-234349400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:234343000-234350600	Genic enhancers	Gastric	stomach
32	chr2:234343000-234351000	Strong transcription	Colonic Mucosa	Colon
33	chr2:234343000-234351800	Strong transcription	Fetal Thymus	thymus
34	chr2:234343000-234352000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:234343000-234352000	Strong transcription	Liver	Liver
36	chr2:234343000-234352000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:234343000-234393000	Strong transcription	Primary T cells from cord blood	blood
38	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:234343200-234345800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:234343200-234347000	Strong transcription	NHEK	skin
41	chr2:234343200-234347200	Strong transcription	Ovary	ovary
42	chr2:234343200-234348200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:234343200-234348400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:234343200-234349600	Strong transcription	HepG2	liver
45	chr2:234343200-234350400	Strong transcription	Rectal Smooth Muscle	rectum
46	chr2:234343200-234350800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:234343200-234351000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:234343200-234351600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:234343200-234351600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:234343200-234352000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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