Variant report

Variant	rs340338
Chromosome Location	chr2:179912942-179912943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10930852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1354385	0.95[ASN][1000 genomes]
rs173110	0.92[ASN][1000 genomes]
rs2592564	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340320	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs340321	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[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	0.95[ASN][1000 genomes]
rs340334	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	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433746	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558039	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179897400-179913000	Weak transcription	Thymus	Thymus
2	chr2:179897400-179913400	Weak transcription	Fetal Thymus	thymus
3	chr2:179897400-179913800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:179897600-179913800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:179907400-179913200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:179908800-179913400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:179909400-179913800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:179909400-179914000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:179909400-179914000	Weak transcription	Pancreas	Pancrea
10	chr2:179909400-179916000	Weak transcription	Spleen	Spleen
11	chr2:179909600-179913400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:179909600-179916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:179910200-179913000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:179910400-179913400	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:179910800-179915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:179911000-179913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:179911200-179913200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:179911200-179914400	Weak transcription	Dnd41	blood
19	chr2:179911400-179913000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:179911400-179913200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:179911400-179913400	Weak transcription	Psoas Muscle	Psoas
22	chr2:179911400-179913400	Weak transcription	HSMM	muscle
23	chr2:179911400-179914400	Weak transcription	Aorta	Aorta
24	chr2:179911600-179914800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:179912000-179913200	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:179912000-179913200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:179912000-179913200	Enhancers	Fetal Intestine Large	intestine
28	chr2:179912000-179915200	Active TSS	Right Atrium	heart
29	chr2:179912400-179913000	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:179912400-179913200	Enhancers	Primary T cells from cord blood	blood
31	chr2:179912400-179913400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:179912400-179913400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:179912400-179913600	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr2:179912400-179914000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr2:179912400-179915400	Active TSS	Fetal Heart	heart
36	chr2:179912600-179913000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:179912600-179913200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:179912600-179914000	Active TSS	Fetal Muscle Leg	muscle
39	chr2:179912600-179914600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr2:179912600-179915000	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:179912600-179915200	Active TSS	Right Ventricle	heart
42	chr2:179912600-179915600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr2:179912600-179915600	Active TSS	HSMMtube	muscle
44	chr2:179912600-179916200	Enhancers	Fetal Kidney	kidney
45	chr2:179912800-179913000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr2:179912800-179913000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr2:179912800-179913400	Weak transcription	Adipose Nuclei	Adipose
48	chr2:179912800-179913600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:179912800-179914000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr2:179912800-179914800	Active TSS	Left Ventricle	heart

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