Variant report

Variant	rs11174538
Chromosome Location	chr12:62937348-62937349
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62936384..62938344-chr12:62940152..62942077,2	MCF-7	breast:
2	chr12:62935650..62938196-chr7:138541897..138543397,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10128830	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs10128959	0.87[ASN][1000 genomes]
rs10161549	0.89[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10219555	0.81[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10219765	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10747963	0.84[JPT][hapmap]
rs10747966	0.82[ASN][1000 genomes]
rs10784299	0.83[ASN][1000 genomes]
rs10784302	0.83[ASN][1000 genomes]
rs10784303	0.82[ASN][1000 genomes]
rs10784306	0.87[ASN][1000 genomes]
rs10784307	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10877860	0.83[ASN][1000 genomes]
rs10877863	0.83[ASN][1000 genomes]
rs10877865	0.85[ASN][1000 genomes]
rs10877866	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10877868	0.89[ASN][1000 genomes]
rs10877869	0.86[ASN][1000 genomes]
rs10877872	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10877873	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10877876	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10877880	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10877883	0.83[ASN][1000 genomes]
rs10877885	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs10877886	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10877887	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877888	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs11174493	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11174507	0.83[ASN][1000 genomes]
rs11174513	0.83[ASN][1000 genomes]
rs11174520	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11174534	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11174540	0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11174541	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11174542	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11174550	0.87[ASN][1000 genomes]
rs11495588	0.80[ASN][1000 genomes]
rs12227568	0.91[ASN][1000 genomes]
rs12300696	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs12305077	0.85[ASN][1000 genomes]
rs12309683	0.82[ASN][1000 genomes]
rs12357	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12371971	0.80[JPT][hapmap]
rs12371972	0.80[JPT][hapmap]
rs12578200	0.81[ASN][1000 genomes]
rs12580048	0.85[ASN][1000 genomes]
rs12581171	0.82[ASN][1000 genomes]
rs12810119	0.82[ASN][1000 genomes]
rs12829103	0.85[ASN][1000 genomes]
rs1498713	0.87[ASN][1000 genomes]
rs2047478	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2047479	0.91[ASN][1000 genomes]
rs4763021	0.81[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4763174	0.86[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4763177	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763179	0.85[ASN][1000 genomes]
rs4763180	0.85[ASN][1000 genomes]
rs6581452	0.84[ASN][1000 genomes]
rs6581454	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7134302	0.90[ASN][1000 genomes]
rs7136993	0.87[ASN][1000 genomes]
rs71453871	0.83[ASN][1000 genomes]
rs7294404	0.85[ASN][1000 genomes]
rs7298782	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7302027	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7308021	0.85[JPT][hapmap]
rs7316612	0.90[ASN][1000 genomes]
rs7957417	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7963657	0.85[ASN][1000 genomes]
rs7975183	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7975560	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv469418	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv559156	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11174538	NXPH4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
2	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
3	chr12:62876000-62937400	Weak transcription	Gastric	stomach
4	chr12:62889200-62949600	Weak transcription	Small Intestine	intestine
5	chr12:62897600-62944000	Weak transcription	Esophagus	oesophagus
6	chr12:62903600-62949800	Weak transcription	NHEK	skin
7	chr12:62906400-62943800	Weak transcription	Aorta	Aorta
8	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:62907400-62940200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:62911400-62944000	Weak transcription	Spleen	Spleen
11	chr12:62914200-62941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:62915800-62971600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:62917000-62940600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
15	chr12:62917400-62960000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:62919800-62970000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:62920000-62950200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:62924400-62945600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:62924400-62949800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:62924400-62969800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:62924600-62938600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:62924800-62967600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:62925400-62949800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:62926000-62945000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:62926000-62951400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:62926200-62949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:62926200-62951400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:62926200-62951600	Strong transcription	Fetal Thymus	thymus
29	chr12:62926200-62951800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:62926200-62955800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:62927400-62941600	Weak transcription	Right Ventricle	heart
32	chr12:62927400-62967400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:62927600-62943400	Weak transcription	HSMMtube	muscle
34	chr12:62928000-62939400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:62928000-62940400	Weak transcription	Brain Angular Gyrus	brain
36	chr12:62928000-62940600	Weak transcription	HMEC	breast
37	chr12:62928000-62941000	Weak transcription	Brain Germinal Matrix	brain
38	chr12:62928000-62942000	Weak transcription	Brain Substantia Nigra	brain
39	chr12:62928000-62943400	Weak transcription	NHLF	lung
40	chr12:62928000-62950400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:62928000-62963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:62928200-62940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:62928200-62950000	Weak transcription	Fetal Brain Male	brain
44	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:62929400-62940200	Weak transcription	Colonic Mucosa	Colon
46	chr12:62929600-62940600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:62929800-62940400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:62930800-62937400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:62931800-62951400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:62932000-62947600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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