Variant report

Variant	rs2288325
Chromosome Location	chr2:179404786-179404787
allele	A/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	chr2:179404526-179405234	K562	blood:	n/a	n/a
2	POLR2A	chr2:179404591-179405102	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:179404748-179405077	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TTN-AS1	TF binding region
ENSG00000270956	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1007025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12614435	0.91[CEU][hapmap]
rs12618265	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12998857	0.91[CEU][hapmap]
rs13005601	0.90[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13009158	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13029629	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13034990	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16866358	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866365	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16866369	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16866373	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16866397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288569	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288571	0.91[CEU][hapmap]
rs2303539	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731746	0.83[CEU][hapmap]
rs3731748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731751	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829748	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755456	0.91[CEU][hapmap]
rs744426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7597154	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs890578	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:179388800-179408600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179388800-179410600	Weak transcription	Colonic Mucosa	Colon
4	chr2:179388800-179411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
9	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:179389400-179405800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:179389400-179408200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:179389400-179408800	Weak transcription	HMEC	breast
14	chr2:179389400-179410000	Weak transcription	Hela-S3	cervix
15	chr2:179389400-179412800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:179389400-179413000	Weak transcription	Fetal Brain Male	brain
17	chr2:179389400-179413400	Weak transcription	NH-A	brain
18	chr2:179389400-179416800	Weak transcription	Stomach Mucosa	stomach
19	chr2:179389400-179417200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:179389400-179417200	Weak transcription	NHDF-Ad	bronchial
21	chr2:179389400-179417200	Weak transcription	NHLF	lung
22	chr2:179389400-179428200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:179390600-179426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:179391200-179419200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:179394800-179412600	Strong transcription	Primary T cells from cord blood	blood
27	chr2:179394800-179413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:179394800-179417600	Strong transcription	HSMMtube	muscle
29	chr2:179394800-179421600	Strong transcription	Left Ventricle	heart
30	chr2:179395400-179414200	Strong transcription	Fetal Thymus	thymus
31	chr2:179395400-179423000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:179395600-179414200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:179395600-179421600	Strong transcription	Fetal Heart	heart
34	chr2:179395800-179411800	Strong transcription	Fetal Muscle Leg	muscle
35	chr2:179395800-179414000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:179395800-179414200	Strong transcription	Dnd41	blood
37	chr2:179396000-179406200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:179396000-179413800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:179396000-179414600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:179396000-179415800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:179396000-179417600	Strong transcription	HSMM	muscle
42	chr2:179396000-179422400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:179396000-179445400	Strong transcription	Right Ventricle	heart
44	chr2:179396200-179405000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:179396200-179405200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:179396200-179405200	Strong transcription	Liver	Liver
47	chr2:179396200-179405200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:179396200-179405400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:179396200-179405400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:179396200-179405600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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