Variant report

Variant	rs12141025
Chromosome Location	chr1:212428571-212428572
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	chr1:212422550..212424543-chr1:212427394..212429711,2	K562	blood:
3	chr1:212427390..212429185-chr1:212456996..212458799,2	K562	blood:
4	chr1:212428170..212430153-chr1:212432529..212434264,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10863959	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119892	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062131	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473321	0.83[CEU][hapmap]
rs1539206	0.83[CEU][hapmap]
rs7513529	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521041	0.85[AFR][1000 genomes]
rs7527863	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531219	0.94[YRI][hapmap];0.85[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12141025	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs12141025	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212416600-212430000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212423600-212431200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:212424200-212428600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:212424200-212429000	Weak transcription	Stomach Mucosa	stomach
5	chr1:212424400-212430800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:212424400-212431200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:212424600-212431000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:212426400-212429000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:212426600-212430800	Enhancers	Fetal Thymus	thymus
10	chr1:212427400-212428800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:212427400-212429600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:212427400-212429800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr1:212427400-212430400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:212427400-212430800	Enhancers	Primary B cells from peripheral blood	blood
15	chr1:212427600-212428800	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:212427600-212429600	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:212427600-212430000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr1:212427600-212430200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr1:212427600-212430400	Flanking Active TSS	Dnd41	blood
20	chr1:212427600-212430600	Enhancers	Thymus	Thymus
21	chr1:212428000-212429000	Enhancers	Adipose Nuclei	Adipose
22	chr1:212428000-212431000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr1:212428200-212428600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:212428200-212428600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr1:212428200-212428600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:212428200-212428600	Enhancers	Esophagus	oesophagus
27	chr1:212428200-212428600	Enhancers	Right Atrium	heart
28	chr1:212428200-212428800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:212428200-212429000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr1:212428200-212429200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:212428200-212429400	Flanking Active TSS	Liver	Liver
32	chr1:212428200-212429400	Enhancers	Brain Angular Gyrus	brain
33	chr1:212428200-212429400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:212428200-212429400	Enhancers	Fetal Intestine Small	intestine
35	chr1:212428200-212429400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:212428200-212429600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr1:212428200-212429600	Enhancers	Fetal Intestine Large	intestine
38	chr1:212428200-212429800	Enhancers	K562	blood
39	chr1:212428200-212430000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:212428200-212430000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:212428200-212430200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:212428200-212430200	Enhancers	Left Ventricle	heart
43	chr1:212428200-212430400	Enhancers	Brain Anterior Caudate	brain
44	chr1:212428200-212430400	Enhancers	GM12878-XiMat	blood
45	chr1:212428200-212430400	Flanking Active TSS	HepG2	liver
46	chr1:212428200-212430600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:212428200-212430600	Enhancers	Lung	lung
48	chr1:212428200-212430800	Enhancers	Spleen	Spleen
49	chr1:212428200-212431000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:212428200-212431800	Enhancers	Pancreas	Pancrea

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