Variant report

Variant	rs1874908
Chromosome Location	chr12:49584030-49584031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:49584000-49584150	BE2_C	brain:	n/a	n/a
2	RFX5	chr12:49580575-49585139	SK-N-SH	brain:	n/a	n/a
3	REST	chr12:49579315-49585380	H1-neurons	neurons:	n/a	chr12:49581154-49581167 chr12:49581154-49581167 chr12:49581714-49581734 chr12:49582472-49582485 chr12:49581151-49581171 chr12:49580352-49580362 chr12:49581151-49581171 chr12:49580345-49580358
4	POLR2A	chr12:49583834-49584538	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:49580549-49584642	H1-neurons	neurons:	n/a	n/a
6	MXI1	chr12:49579985-49584758	SK-N-SH	brain:	n/a	n/a
7	TAF1	chr12:49583960-49584544	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49580754..49584871-chr12:49657957..49661825,4	MCF-7	breast:
2	chr12:49503855..49506778-chr12:49583958..49586490,2	K562	blood:
3	chr12:49581100..49585285-chr12:49656726..49660800,10	MCF-7	breast:
4	chr12:49583300..49585414-chr12:49665857..49667533,2	K562	blood:
5	chr12:49522685..49527255-chr12:49580115..49585539,18	MCF-7	breast:
6	chr12:49581145..49584248-chr12:49657471..49660758,4	K562	blood:
7	chr12:49522957..49526705-chr12:49580771..49584514,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TUBA1C-3	chr12:49582863-49584217	NONHSAT028086

Variant related genes	Relation type
TUBA1A	TF binding region
ENSG00000258017	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1039225	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1056875	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10747561	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs10747562	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap]
rs10747563	0.94[CHB][hapmap]
rs10783302	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs10783307	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875922	0.89[EUR][1000 genomes]
rs10875924	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875925	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875927	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875929	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875930	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875931	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875934	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs11168857	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs11168862	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap]
rs11168874	0.87[EUR][1000 genomes]
rs11168882	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168883	0.83[EUR][1000 genomes]
rs11168884	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168885	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168888	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168890	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168893	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs11168894	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168895	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168901	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168902	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168903	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168904	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168909	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168910	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12227296	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12227610	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12227770	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229524	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229529	0.85[EUR][1000 genomes]
rs12306494	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12318740	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579015	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1476137	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1476138	0.84[EUR][1000 genomes]
rs1991427	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991428	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2016107	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2047101	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2114845	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2114846	0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162643	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2162644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241727	0.84[EUR][1000 genomes]
rs2279596	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs2334930	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2334931	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2878287	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35884657	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741621	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs57853986	0.84[EUR][1000 genomes]
rs58336603	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58711211	0.82[EUR][1000 genomes]
rs6580701	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580703	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs697624	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7137978	0.82[EUR][1000 genomes]
rs7306084	0.94[CHB][hapmap]
rs73110168	0.85[EUR][1000 genomes]
rs7311346	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs731350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs7953169	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954521	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954530	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7957998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958241	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7958572	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs7959497	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap]
rs7969963	0.83[EUR][1000 genomes]
rs7969967	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7976890	0.83[EUR][1000 genomes]
rs7978448	0.87[CEU][hapmap]
rs9325145	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs9739878	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788139	0.82[EUR][1000 genomes]
rs9788140	0.82[EUR][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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1874908	RHEBL1	cis	parietal	SCAN
rs1874908	OR10AD1	cis	parietal	SCAN
rs1874908	METTL7A	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49579600-49584400	Active TSS	Brain Angular Gyrus	brain
2	chr12:49580400-49584200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:49580400-49584600	Active TSS	Fetal Brain Male	brain
4	chr12:49580600-49584200	Active TSS	Brain Anterior Caudate	brain
5	chr12:49582800-49584600	Active TSS	Fetal Brain Female	brain
6	chr12:49583000-49584200	Active TSS	Right Atrium	heart
7	chr12:49583000-49584800	Active TSS	Brain Germinal Matrix	brain
8	chr12:49583000-49592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49583200-49584200	Weak transcription	Lung	lung
10	chr12:49583200-49584400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:49583200-49595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:49583400-49584200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:49583400-49584200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr12:49583400-49584400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:49583400-49584600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr12:49583400-49591400	Weak transcription	K562	blood
17	chr12:49583400-49595800	Weak transcription	Ovary	ovary
18	chr12:49583600-49584200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:49583600-49584200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:49583600-49584200	Enhancers	A549	lung
21	chr12:49583600-49584200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr12:49583600-49584400	Enhancers	Dnd41	blood
23	chr12:49583600-49584600	Enhancers	HSMM	muscle
24	chr12:49583600-49585200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:49583600-49588800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:49583600-49592200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:49583600-49592400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:49583600-49592400	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:49583600-49594600	Weak transcription	Fetal Kidney	kidney
30	chr12:49583600-49595800	Weak transcription	Aorta	Aorta
31	chr12:49583600-49595800	Weak transcription	Fetal Thymus	thymus
32	chr12:49583800-49584200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:49583800-49584200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:49583800-49584200	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr12:49583800-49584200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr12:49583800-49584200	Enhancers	HUVEC	blood vessel
37	chr12:49583800-49584400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:49583800-49584400	Enhancers	NHDF-Ad	bronchial
39	chr12:49583800-49589200	Weak transcription	Adipose Nuclei	Adipose
40	chr12:49583800-49592400	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:49583800-49592400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:49584000-49584200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:49584000-49584200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:49584000-49584200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:49584000-49584200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr12:49584000-49584200	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr12:49584000-49584200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr12:49584000-49584200	Flanking Active TSS	HSMMtube	muscle
49	chr12:49584000-49584200	Enhancers	NH-A	brain
50	chr12:49584000-49584400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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