Variant report

Variant	rs1354385
Chromosome Location	chr2:179911417-179911418
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10084229	1.00[CHB][hapmap];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	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10439300	1.00[JPT][hapmap]
rs10803924	1.00[JPT][hapmap]
rs10930852	0.87[ASN][1000 genomes]
rs10930855	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10930856	1.00[CHB][hapmap]
rs10930857	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12621115	0.90[JPT][hapmap]
rs12693175	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12693179	0.90[JPT][hapmap]
rs12987285	0.90[JPT][hapmap]
rs12997079	1.00[CHB][hapmap]
rs13022867	1.00[CHB][hapmap]
rs13029576	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13382185	0.90[JPT][hapmap]
rs13396334	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs13404037	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs173110	0.87[ASN][1000 genomes]
rs17363260	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17363267	1.00[CHB][hapmap]
rs2009639	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2289993	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2289994	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2592564	0.95[ASN][1000 genomes]
rs2655158	0.95[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs340321	0.92[ASN][1000 genomes]
rs340326	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340328	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340329	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs340330	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340332	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340334	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340338	0.95[ASN][1000 genomes]
rs340349	0.90[ASN][1000 genomes]
rs340350	0.90[ASN][1000 genomes]
rs4893863	0.95[ASN][1000 genomes]
rs6433746	0.95[ASN][1000 genomes]
rs7558039	0.95[ASN][1000 genomes]
rs7598203	0.95[ASN][1000 genomes]
rs7601366	0.89[JPT][hapmap]
rs924801	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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:49 , 50 per page) page: 1

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	chr2:179897600-179912600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:179897600-179913800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:179906800-179911600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:179907400-179913200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:179907600-179912800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:179908800-179913400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:179909400-179912400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:179909400-179913800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:179909400-179914000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:179909400-179914000	Weak transcription	Pancreas	Pancrea
14	chr2:179909400-179916000	Weak transcription	Spleen	Spleen
15	chr2:179909600-179912000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:179909600-179912400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:179909600-179913400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:179909600-179916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:179909800-179912000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:179910200-179913000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:179910400-179911600	ZNF genes & repeats	GM12878-XiMat	blood
22	chr2:179910400-179912800	Enhancers	Primary B cells from cord blood	blood
23	chr2:179910400-179913400	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:179910800-179912800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:179910800-179915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:179911000-179911600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:179911000-179911600	Strong transcription	HSMMtube	muscle
28	chr2:179911000-179911800	Strong transcription	Primary T cells from cord blood	blood
29	chr2:179911000-179913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:179911200-179912400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr2:179911200-179912600	Weak transcription	Adipose Nuclei	Adipose
32	chr2:179911200-179912800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:179911200-179913200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:179911200-179914400	Weak transcription	Dnd41	blood
35	chr2:179911400-179911600	Active TSS	Fetal Heart	heart
36	chr2:179911400-179912000	Weak transcription	Fetal Intestine Large	intestine
37	chr2:179911400-179912400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:179911400-179912600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:179911400-179912600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:179911400-179912600	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:179911400-179912600	Weak transcription	Right Ventricle	heart
42	chr2:179911400-179912800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:179911400-179912800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:179911400-179912800	Weak transcription	Left Ventricle	heart
45	chr2:179911400-179913000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:179911400-179913200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:179911400-179913400	Weak transcription	Psoas Muscle	Psoas
48	chr2:179911400-179913400	Weak transcription	HSMM	muscle
49	chr2:179911400-179914400	Weak transcription	Aorta	Aorta

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