Variant report

Variant	rs340334
Chromosome Location	chr2:179915121-179915122
allele	C/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	TBP	chr2:179913708-179915283	GM12878	blood:	n/a	n/a
2	KAP1	chr2:179914534-179915234	U2OS	brain:	n/a	n/a
3	GATA3	chr2:179914732-179915243	SK-N-SH	brain:	n/a	chr2:179914959-179914971 chr2:179914960-179914970 chr2:179914961-179914970 chr2:179914957-179914973 chr2:179914908-179914919
4	PML	chr2:179913428-179915145	GM12878	blood:	n/a	chr2:179914409-179914417
5	GATA2	chr2:179914660-179915134	SH-SY5Y	brain:	n/a	chr2:179914959-179914971 chr2:179914960-179914970 chr2:179914961-179914970 chr2:179914957-179914973 chr2:179914908-179914919
6	GATA3	chr2:179914830-179915154	SH-SY5Y	brain:	n/a	chr2:179914959-179914971 chr2:179914960-179914970 chr2:179914961-179914970 chr2:179914957-179914973 chr2:179914908-179914919
7	KAP1	chr2:179914434-179915291	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
CCDC141	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10084229	0.89[JPT][hapmap]
rs10164707	0.90[JPT][hapmap]
rs10164814	0.88[JPT][hapmap]
rs10181464	0.90[JPT][hapmap]
rs10188759	0.90[JPT][hapmap]
rs10208593	0.89[JPT][hapmap]
rs10439300	1.00[JPT][hapmap]
rs10803924	1.00[JPT][hapmap]
rs10930852	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930855	0.89[JPT][hapmap]
rs10930857	0.86[JPT][hapmap]
rs12621115	0.90[JPT][hapmap]
rs12693175	0.89[JPT][hapmap]
rs12693179	0.90[JPT][hapmap]
rs12987285	0.90[JPT][hapmap]
rs13029576	0.88[JPT][hapmap]
rs13382185	0.90[JPT][hapmap]
rs13396334	0.89[JPT][hapmap]
rs13404037	0.89[JPT][hapmap]
rs1354385	0.95[ASN][1000 genomes]
rs173110	0.92[ASN][1000 genomes]
rs17363260	0.89[JPT][hapmap]
rs2289993	0.89[JPT][hapmap]
rs2289994	0.89[JPT][hapmap]
rs2592564	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655158	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs340321	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340326	0.88[ASN][1000 genomes]
rs340328	0.95[ASN][1000 genomes]
rs340329	0.84[ASN][1000 genomes]
rs340332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340338	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340349	0.95[ASN][1000 genomes]
rs340350	0.95[ASN][1000 genomes]
rs4893863	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433746	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558039	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598203	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601366	0.89[JPT][hapmap]
rs924801	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv875464	chr2:179843612-179939493	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875465	chr2:179843612-179966804	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv508184	chr2:179896384-179965419	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179909400-179916000	Weak transcription	Spleen	Spleen
2	chr2:179909600-179916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:179910800-179915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:179912000-179915200	Active TSS	Right Atrium	heart
5	chr2:179912400-179915400	Active TSS	Fetal Heart	heart
6	chr2:179912600-179915200	Active TSS	Right Ventricle	heart
7	chr2:179912600-179915600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:179912600-179915600	Active TSS	HSMMtube	muscle
9	chr2:179912600-179916200	Enhancers	Fetal Kidney	kidney
10	chr2:179912800-179915200	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr2:179912800-179916000	Active TSS	Fetal Muscle Trunk	muscle
12	chr2:179913200-179915200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr2:179913200-179915200	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr2:179913400-179916400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:179913400-179916400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:179913600-179915200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr2:179913600-179917000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:179913800-179915200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr2:179913800-179915200	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr2:179913800-179915200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:179913800-179916200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:179913800-179916200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:179913800-179916200	Enhancers	Fetal Lung	lung
24	chr2:179914000-179915200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr2:179914200-179915200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:179914200-179915200	Active TSS	Psoas Muscle	Psoas
27	chr2:179914400-179915200	Flanking Active TSS	Fetal Thymus	thymus
28	chr2:179914400-179915800	Enhancers	HepG2	liver
29	chr2:179914600-179915400	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:179914600-179915600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr2:179914600-179916000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:179914600-179916000	Enhancers	Colon Smooth Muscle	Colon
33	chr2:179914600-179916000	Weak transcription	Placenta	Placenta
34	chr2:179914600-179916200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:179914600-179916400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr2:179914800-179915200	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr2:179914800-179915400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:179914800-179915600	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr2:179914800-179915800	Weak transcription	Liver	Liver
40	chr2:179914800-179915800	Weak transcription	Pancreas	Pancrea
41	chr2:179914800-179915800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:179914800-179916000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:179914800-179916000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:179914800-179916000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:179914800-179916000	Weak transcription	Left Ventricle	heart
46	chr2:179914800-179916200	Enhancers	Fetal Intestine Small	intestine
47	chr2:179914800-179916200	Enhancers	Stomach Smooth Muscle	stomach
48	chr2:179914800-179917000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:179915000-179915200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr2:179915000-179915200	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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