Variant report

Variant	rs11173121
Chromosome Location	chr12:60113674-60113675
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-272B17.2.1-2	chr12:60113479-60113725	NONHSAT029055

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10459250	0.90[CHB][hapmap]
rs10783997	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877329	0.92[CHB][hapmap]
rs10877330	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877348	0.92[EUR][1000 genomes]
rs11173115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11173138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11173183	0.96[EUR][1000 genomes]
rs11173186	0.96[EUR][1000 genomes]
rs11611304	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11611808	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12229478	0.92[CHB][hapmap]
rs12231378	0.92[CHB][hapmap]
rs12581981	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17572569	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs17573052	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17650140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3847656	0.92[CHB][hapmap]
rs4323908	0.93[EUR][1000 genomes]
rs55863604	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55869967	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56053489	0.91[ASN][1000 genomes]
rs56410712	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs73111818	0.98[ASN][1000 genomes]
rs73113308	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7971953	0.91[CHB][hapmap]
rs7972065	0.88[EUR][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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:60089400-60126000	Weak transcription	Left Ventricle	heart
3	chr12:60093800-60126600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:60094000-60127200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:60094200-60127200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:60095400-60114400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:60098000-60117000	Weak transcription	Psoas Muscle	Psoas
8	chr12:60099200-60126600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:60099400-60130400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:60100400-60126400	Weak transcription	Primary B cells from cord blood	blood
13	chr12:60100600-60127200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:60101800-60122000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:60104200-60138000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:60105600-60129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:60106800-60117800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:60109400-60121800	Weak transcription	Right Ventricle	heart
19	chr12:60109400-60126600	Weak transcription	Primary T cells from cord blood	blood
20	chr12:60110200-60141400	Weak transcription	Dnd41	blood
21	chr12:60112600-60117400	Weak transcription	Liver	Liver
22	chr12:60112600-60126800	Weak transcription	Adipose Nuclei	Adipose
23	chr12:60113000-60143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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