Variant report

Variant	rs2288128
Chromosome Location	chr12:29468987-29468988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29462295..29465782-chr12:29467175..29469867,4	K562	blood:
2	chr12:29462295..29464942-chr12:29467954..29469867,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1006410	1.00[ASW][hapmap];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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1072724	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743652	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs10743656	0.90[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10771514	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10771517	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10771520	0.80[ASN][1000 genomes]
rs10771521	0.81[ASN][1000 genomes]
rs10843376	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10843385	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843399	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10843401	0.81[ASN][1000 genomes]
rs11050147	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050149	0.83[EUR][1000 genomes]
rs11050168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12301475	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12578931	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581107	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17715086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1836861	0.92[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2016832	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288129	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350315	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782505	1.00[ASW][hapmap];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[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782510	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3948497	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4277150	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4931171	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4931174	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6487807	0.84[CEU][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7298031	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7299283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7302986	0.81[ASN][1000 genomes]
rs7308534	0.91[YRI][hapmap]
rs7313552	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7315346	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7358667	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7953619	1.00[YRI][hapmap]
rs7956305	0.81[CEU][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7959145	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7961943	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7964831	1.00[ASW][hapmap];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[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980218	0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs986072	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1795347	chr12:29458556-29471835	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2288128	RP11-996F15.2	cis	Thyroid	GTEx
rs2288128	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs2288128	IFLTD1	cis	parietal	SCAN
rs2288128	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
3	chr12:29439600-29469400	Weak transcription	NH-A	brain
4	chr12:29449600-29470800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:29452800-29494200	Weak transcription	Lung	lung
6	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
7	chr12:29453800-29480000	Weak transcription	Gastric	stomach
8	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
9	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
10	chr12:29456000-29469600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:29456600-29471000	Weak transcription	Fetal Intestine Small	intestine
12	chr12:29457600-29470600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:29459400-29471400	Weak transcription	Liver	Liver
14	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:29459600-29472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
17	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
18	chr12:29460800-29470000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
21	chr12:29463200-29470000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:29463600-29474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:29463800-29469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:29463800-29475400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
26	chr12:29464200-29470000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:29464600-29474800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:29465000-29469600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
30	chr12:29465400-29470000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:29465600-29469600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:29465600-29471000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:29465800-29472800	Weak transcription	NHDF-Ad	bronchial
34	chr12:29466000-29469600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:29466000-29470400	Weak transcription	Dnd41	blood
36	chr12:29466000-29474400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:29466000-29474600	Weak transcription	Placenta	Placenta
38	chr12:29466200-29469200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:29466200-29470600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:29466200-29470600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:29466200-29472600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:29466400-29469600	Weak transcription	HUVEC	blood vessel
44	chr12:29466800-29469000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:29467000-29469600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:29467200-29470800	Active TSS	Right Ventricle	heart
47	chr12:29467200-29472800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr12:29467200-29473400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:29467200-29475800	Weak transcription	Pancreas	Pancrea
50	chr12:29467400-29469400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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