Variant report

Variant	rs2664050
Chromosome Location	chr6:142889552-142889553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIVEP2-7	chr6:142889285-142891213	NONHSAT115318

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1070576	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1070577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1098067	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1098071	0.93[ASN][1000 genomes]
rs13217677	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1417359	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs171913	0.91[ASN][1000 genomes]
rs171914	0.90[ASN][1000 genomes]
rs263114	0.93[ASN][1000 genomes]
rs263120	0.99[ASN][1000 genomes]
rs263121	0.99[ASN][1000 genomes]
rs263154	0.94[ASN][1000 genomes]
rs263166	0.96[ASN][1000 genomes]
rs263175	0.89[ASN][1000 genomes]
rs35781078	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56077882	0.82[EUR][1000 genomes]
rs67446783	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6906209	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6921853	0.87[EUR][1000 genomes]
rs702289	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs702290	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs702291	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs702292	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs702293	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs702294	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs702295	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs702296	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs702298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762733	0.82[AFR][1000 genomes]
rs844443	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs863432	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9386003	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9390007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9390009	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9390011	0.91[EUR][1000 genomes]
rs9403400	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9496420	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9496423	0.86[EUR][1000 genomes]
rs9496427	0.87[EUR][1000 genomes]
rs9496432	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9496434	0.82[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv520479	chr6:142869099-142908146	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142883400-142890400	Weak transcription	Stomach Mucosa	stomach
2	chr6:142884200-142890200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:142885200-142891000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:142887400-142890200	Enhancers	Primary T cells from cord blood	blood
5	chr6:142887600-142892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr6:142887600-142892200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:142887600-142892200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:142887600-142892600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:142887800-142890200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:142887800-142890800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:142887800-142892000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:142887800-142892200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:142888000-142891400	Enhancers	HMEC	breast
14	chr6:142888000-142892800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:142888200-142892000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr6:142888200-142892200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:142888400-142889600	Weak transcription	NHDF-Ad	bronchial
18	chr6:142888400-142891800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:142888400-142893400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:142888600-142890000	Weak transcription	Fetal Lung	lung
21	chr6:142888600-142890200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:142888600-142892000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:142888800-142889600	Weak transcription	HSMMtube	muscle
24	chr6:142888800-142890000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:142888800-142891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:142888800-142892000	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:142889000-142889600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:142889000-142891400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:142889200-142892200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:142889200-142892600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:142889200-142893600	Enhancers	Dnd41	blood
32	chr6:142889400-142889600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:142889400-142890400	Enhancers	NH-A	brain
34	chr6:142889400-142891200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:142889400-142891800	Enhancers	Fetal Thymus	thymus
36	chr6:142889400-142892600	Enhancers	HSMM	muscle
37	chr6:142889400-142893200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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