Variant report

Variant	rs10774898
Chromosome Location	chr12:117468873-117468874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117468241..117470806-chr12:117471546..117474082,2	K562	blood:
2	chr12:117462045..117463688-chr12:117467328..117470013,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TESC-4	chr12:117468512-117468878	NONHSAT030977

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10735100	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10735101	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10735102	0.93[ASW][hapmap]
rs10774895	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10850730	0.84[EUR][1000 genomes]
rs10850734	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850742	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10850747	0.83[JPT][hapmap]
rs10850751	0.88[JPT][hapmap]
rs11068264	0.86[ASW][hapmap]
rs11068276	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068277	0.81[ASW][hapmap]
rs11068292	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11068296	0.87[ASW][hapmap]
rs11834817	0.88[JPT][hapmap]
rs1472523	0.88[JPT][hapmap]
rs2062528	0.94[JPT][hapmap]
rs2173654	0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2291916	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2393111	0.81[ASW][hapmap]
rs2393113	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4076700	0.81[ASW][hapmap]
rs4562927	0.93[ASW][hapmap]
rs4766815	0.93[ASW][hapmap]
rs4766816	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4766823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767474	0.93[ASW][hapmap]
rs4767477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4767484	0.93[ASW][hapmap]
rs4767486	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767489	0.93[ASW][hapmap]
rs6490103	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6490106	0.83[JPT][hapmap]
rs7133090	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7297303	0.88[JPT][hapmap]
rs7297848	0.87[ASW][hapmap]
rs7302127	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs7486428	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7487081	0.83[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7958680	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962875	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7964668	0.88[JPT][hapmap]
rs9634171	0.82[CHD][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10774898	TESC	cis	lymphoblastoid	seeQTL
rs10774898	TESC	cis	parietal	SCAN
rs10774898	C12orf49	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
2	chr12:117452400-117469000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:117452800-117470200	Weak transcription	HUVEC	blood vessel
4	chr12:117452800-117479000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:117453600-117470600	Weak transcription	Psoas Muscle	Psoas
6	chr12:117457200-117469200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:117457600-117469200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:117458600-117469200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:117458800-117469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:117459600-117469200	Strong transcription	Osteobl	bone
11	chr12:117461000-117469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:117461200-117469200	Strong transcription	Fetal Thymus	thymus
13	chr12:117461400-117469200	Strong transcription	Lung	lung
14	chr12:117461600-117470600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:117461800-117469200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:117461800-117469800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:117462000-117477400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:117463200-117470200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:117463200-117471000	Weak transcription	Right Atrium	heart
20	chr12:117463400-117470200	Weak transcription	GM12878-XiMat	blood
21	chr12:117463600-117470600	Weak transcription	Fetal Kidney	kidney
22	chr12:117463800-117469000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:117463800-117469000	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:117464000-117469000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:117464000-117469000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:117464000-117469200	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:117464000-117469400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr12:117464000-117469600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:117464000-117470000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:117464000-117470800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:117464000-117471800	Weak transcription	K562	blood
32	chr12:117464400-117469600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:117464600-117471000	Weak transcription	HSMM	muscle
34	chr12:117464800-117469200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:117465600-117470600	Weak transcription	Brain Angular Gyrus	brain
36	chr12:117466000-117470400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:117466200-117474600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:117466400-117469400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:117466400-117469800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:117466400-117470000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:117466400-117470400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:117466400-117470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:117466400-117470400	Weak transcription	Brain Anterior Caudate	brain
44	chr12:117466400-117470400	Weak transcription	Brain Germinal Matrix	brain
45	chr12:117466400-117470400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:117466400-117470600	Weak transcription	Ovary	ovary
47	chr12:117466400-117470800	Weak transcription	Colonic Mucosa	Colon
48	chr12:117466400-117470800	Weak transcription	Gastric	stomach
49	chr12:117466400-117470800	Weak transcription	Right Ventricle	heart
50	chr12:117466400-117471000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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