Variant report

Variant	rs12728266
Chromosome Location	chr1:212430756-212430757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212427899..212432292-chr1:212432529..212438731,7	K562	blood:
2	chr1:212428875..212432292-chr1:212434801..212437724,6	K562	blood:
3	chr1:212409597..212412349-chr1:212428867..212431226,2	K562	blood:
4	chr1:212423429..212425837-chr1:212429181..212431560,2	K562	blood:

Variant related genes	Relation type
ENSG00000226251	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10494951	0.90[TSI][hapmap]
rs10863960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863961	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10863963	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11119899	0.96[ASN][1000 genomes]
rs11119919	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11119920	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11119924	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11119930	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11576437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11579999	0.86[ASN][1000 genomes]
rs11580285	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585215	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11587555	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11589817	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590242	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap]
rs11590672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12060029	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12064553	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12066356	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12722832	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12726409	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12727947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730098	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12734895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12743785	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12745269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12747025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12756678	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1470390	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1493600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1530451	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17721302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2120770	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs2297306	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2358448	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2358454	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs34212128	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34244392	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34447409	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34740542	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35872305	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55814152	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6661987	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6667199	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6676208	0.87[TSI][hapmap]
rs71646153	0.83[EUR][1000 genomes]
rs7518399	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7521041	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531219	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs968531	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs968532	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12728266	RP11-15I11.3	cis	lung	GTEx
rs12728266	RP11-15I11.3	cis	Nerve Tibial	GTEx
rs12728266	RP11-15I11.3	cis	Thyroid	GTEx
rs12728266	KCNH1	cis	cerebellum	SCAN
rs12728266	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212423600-212431200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr1:212424400-212430800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:212424400-212431200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:212424600-212431000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:212426600-212430800	Enhancers	Fetal Thymus	thymus
6	chr1:212427400-212430800	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:212428000-212431000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr1:212428200-212430800	Enhancers	Spleen	Spleen
9	chr1:212428200-212431000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:212428200-212431800	Enhancers	Pancreas	Pancrea
11	chr1:212428400-212430800	Enhancers	Right Ventricle	heart
12	chr1:212428600-212434000	Weak transcription	Esophagus	oesophagus
13	chr1:212428800-212434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:212429200-212434200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:212429200-212434400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:212429400-212431200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:212429400-212431200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:212429400-212431600	Enhancers	Liver	Liver
19	chr1:212429400-212432600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:212429400-212434000	Weak transcription	Stomach Mucosa	stomach
21	chr1:212429400-212434800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:212429400-212435600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:212429600-212430800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:212429600-212433000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:212429600-212434000	Weak transcription	Fetal Intestine Large	intestine
26	chr1:212429600-212434200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:212429800-212430800	Enhancers	Right Atrium	heart
28	chr1:212429800-212431400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:212429800-212432400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:212429800-212434000	Weak transcription	K562	blood
31	chr1:212430000-212431400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:212430000-212431600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:212430000-212431600	Weak transcription	Small Intestine	intestine
34	chr1:212430000-212431800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:212430000-212433600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:212430000-212433800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:212430200-212430800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:212430200-212430800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:212430200-212431400	Weak transcription	Gastric	stomach
40	chr1:212430200-212433200	Enhancers	Primary T cells from cord blood	blood
41	chr1:212430200-212434600	Weak transcription	Left Ventricle	heart
42	chr1:212430400-212430800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:212430400-212430800	Enhancers	Dnd41	blood
44	chr1:212430400-212431000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:212430400-212431000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:212430400-212431400	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:212430400-212435600	Enhancers	HepG2	liver
48	chr1:212430600-212431400	Enhancers	Primary B cells from cord blood	blood
49	chr1:212430600-212431600	Weak transcription	Thymus	Thymus
50	chr1:212430600-212434000	Weak transcription	Lung	lung

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