Variant report

Variant	rs601142
Chromosome Location	chr11:75308447-75308448
allele	A/G
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	chr11:75308414-75309158	A549	lung:	n/a	chr11:75308870-75308886 chr11:75308869-75308887 chr11:75308874-75308882 chr11:75308871-75308892
2	CTCF	chr11:75308420-75308570	HCM	heart:	n/a	n/a
3	CTCF	chr11:75308420-75308570	BJ	skin:	n/a	n/a
4	CTCF	chr11:75308360-75308510	HMEC	breast:	n/a	n/a
5	CTCF	chr11:75308379-75309410	SK-N-SH	brain:	n/a	chr11:75308870-75308886 chr11:75308869-75308887 chr11:75308874-75308882 chr11:75308871-75308892

No.	Distal block	Cell Line	Cell type
1	chr11:75287960..75288894-chr11:75308366..75309178,2	K562	blood:
2	chr11:75272209..75273815-chr11:75308377..75311423,3	MCF-7	breast:
3	chr11:75274194..75276398-chr11:75306553..75308654,2	K562	blood:
4	chr11:75308426..75309326-chr11:75511889..75512461,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255434	TF binding region
ENSG00000149257	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1793395	0.81[JPT][hapmap]
rs2015782	0.90[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs2511005	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs544997	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs581522	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584046	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs585433	0.86[JPT][hapmap]
rs588955	0.86[JPT][hapmap]
rs589063	0.86[JPT][hapmap]
rs599816	0.86[JPT][hapmap]
rs601293	0.86[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs609131	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611221	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617449	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs629176	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636418	0.86[JPT][hapmap]
rs640277	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs642002	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644388	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648930	1.00[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];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652524	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664133	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs678320	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678874	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683195	0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs684644	0.81[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs601142	CTD-2530H12.4	cis	Artery Tibial	GTEx
rs601142	C11orf30	cis	parietal	SCAN
rs601142	SLCO2B1	cis	cerebellum	SCAN
rs601142	PGM2L1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75295400-75329600	Weak transcription	Aorta	Aorta
2	chr11:75295600-75310800	Weak transcription	Right Atrium	heart
3	chr11:75295600-75314200	Weak transcription	Lung	lung
4	chr11:75295800-75316400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:75296600-75321000	Weak transcription	Ovary	ovary
6	chr11:75301600-75313800	Weak transcription	Fetal Lung	lung
7	chr11:75302800-75312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:75304800-75309200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:75305000-75308800	Enhancers	K562	blood
10	chr11:75305000-75328800	Weak transcription	Pancreas	Pancrea
11	chr11:75305200-75309400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:75305400-75309000	Weak transcription	Fetal Intestine Large	intestine
13	chr11:75305600-75308800	Weak transcription	Fetal Brain Male	brain
14	chr11:75305600-75316000	Weak transcription	Brain Angular Gyrus	brain
15	chr11:75305800-75313400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:75305800-75316000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:75305800-75346200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:75306000-75326200	Weak transcription	Brain Hippocampus Middle	brain
19	chr11:75306000-75326200	Weak transcription	Brain Substantia Nigra	brain
20	chr11:75306200-75312600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:75306400-75312600	Weak transcription	Fetal Stomach	stomach
22	chr11:75306400-75313400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:75306400-75323600	Weak transcription	Spleen	Spleen
24	chr11:75306600-75309600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:75306600-75324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:75306800-75308800	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:75306800-75309000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:75307000-75316000	Weak transcription	Brain Anterior Caudate	brain
29	chr11:75307600-75308800	Enhancers	Duodenum Mucosa	Duodenum
30	chr11:75307600-75309200	Enhancers	Brain Germinal Matrix	brain
31	chr11:75307800-75309600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr11:75307800-75310200	Enhancers	Fetal Intestine Small	intestine
33	chr11:75308000-75309000	Weak transcription	Fetal Heart	heart
34	chr11:75308400-75309000	Enhancers	Fetal Brain Female	brain
35	chr11:75308400-75309800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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