Variant report

Variant	rs13236704
Chromosome Location	chr7:140712618-140712619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:140712510-140712858	MCF10A-Er-Src	breast:	n/a	n/a
2	RAD21	chr7:140711261-140712680	SK-N-SH	brain:	n/a	n/a
3	FOS	chr7:140712541-140712864	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF384	chr7:140711701-140712716	GM12878	blood:	n/a	n/a
5	JUND	chr7:140712578-140713120	HepG2	liver:	n/a	n/a
6	FOS	chr7:140712509-140712913	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr7:140712540-140712690	HEEpiC	esophagus:	n/a	n/a
8	MAFK	chr7:140711964-140712862	IMR90	lung:	n/a	n/a
9	STAT3	chr7:140711920-140712811	MCF10A-Er-Src	breast:	n/a	n/a
10	SMC3	chr7:140711797-140713610	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr7:140712532-140712768	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr7:140712352-140712825	IMR90	lung:	n/a	n/a
13	FOS	chr7:140712555-140712898	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140703503..140705840-chr7:140711897..140713642,2	MCF-7	breast:
2	chr7:140395386..140400852-chr7:140710628..140716984,11	MCF-7	breast:
3	chr7:140509026..140511710-chr7:140712128..140713632,2	K562	blood:
4	chr7:140394845..140398499-chr7:140712009..140715919,6	MCF-7	breast:
5	chr7:140425846..140426811-chr7:140711662..140712678,3	MCF-7	breast:
6	chr7:140621424..140625988-chr7:140712136..140716057,7	K562	blood:
7	chr7:140394719..140399884-chr7:140712014..140716961,9	K562	blood:

No data

Variant related genes	Relation type
MRPS33	TF binding region
ENSG00000240889	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000157764	Chromatin interaction
ENSG00000273081	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10215245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10255167	0.84[EUR][1000 genomes]
rs10268118	0.84[EUR][1000 genomes]
rs1044927	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1089264	0.95[ASN][1000 genomes]
rs10952364	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12538296	0.86[EUR][1000 genomes]
rs12703284	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13234490	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];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860720	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961288	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2079978	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688430	0.95[ASN][1000 genomes]
rs3805116	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs3852286	0.84[EUR][1000 genomes]
rs3864527	0.84[EUR][1000 genomes]
rs38715	1.00[CHB][hapmap]
rs38720	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs38722	1.00[CHB][hapmap]
rs38723	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs38726	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs38730	0.89[ASN][1000 genomes]
rs38731	0.89[ASN][1000 genomes]
rs38734	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs38736	0.91[ASN][1000 genomes]
rs38739	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs38740	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs4726196	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4726225	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs490810	0.87[ASN][1000 genomes]
rs512177	0.91[ASN][1000 genomes]
rs512509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs528957	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs533441	0.91[ASN][1000 genomes]
rs544081	0.89[ASN][1000 genomes]
rs545121	0.91[ASN][1000 genomes]
rs557962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs569584	0.89[ASN][1000 genomes]
rs579518	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6464217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6464260	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464284	0.87[ASN][1000 genomes]
rs6662	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6967214	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971577	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7792447	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801117	0.95[ASN][1000 genomes]
rs801121	0.95[ASN][1000 genomes]
rs801127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs801155	0.89[ASN][1000 genomes]
rs801159	0.91[ASN][1000 genomes]
rs9274	1.00[CHB][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	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13236704	ADCK2	cis	cerebellum	SCAN
rs13236704	IFI16	trans	cerebellum	SCAN
rs13236704	YIPF5	trans	cerebellum	SCAN
rs13236704	CLEC5A	cis	cerebellum	SCAN
rs13236704	MRPS33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140698600-140713000	Weak transcription	Psoas Muscle	Psoas
2	chr7:140699600-140713800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:140701400-140713400	Weak transcription	NHLF	lung
4	chr7:140702800-140713200	Weak transcription	HSMMtube	muscle
5	chr7:140703200-140713800	Weak transcription	Stomach Mucosa	stomach
6	chr7:140703400-140713800	Weak transcription	Gastric	stomach
7	chr7:140703600-140713800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:140703600-140713800	Weak transcription	Lung	lung
9	chr7:140704000-140713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:140705000-140713600	Weak transcription	NH-A	brain
11	chr7:140705200-140713200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:140705200-140713200	Weak transcription	Brain Germinal Matrix	brain
13	chr7:140705200-140713800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:140705400-140713000	Weak transcription	Dnd41	blood
15	chr7:140705400-140713600	Weak transcription	HUVEC	blood vessel
16	chr7:140706800-140713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:140707200-140713200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:140707200-140713800	Weak transcription	Small Intestine	intestine
19	chr7:140707400-140713600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:140707400-140713600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:140707600-140713400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:140707600-140713600	Weak transcription	Fetal Brain Male	brain
23	chr7:140707600-140713800	Weak transcription	Aorta	Aorta
24	chr7:140707600-140713800	Weak transcription	Spleen	Spleen
25	chr7:140707800-140713000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:140707800-140713200	Weak transcription	Thymus	Thymus
27	chr7:140707800-140713800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:140707800-140713800	Weak transcription	Esophagus	oesophagus
29	chr7:140707800-140713800	Weak transcription	Pancreas	Pancrea
30	chr7:140707800-140714000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:140708000-140713800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:140708200-140713400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:140708400-140713200	Weak transcription	Brain Substantia Nigra	brain
34	chr7:140708400-140713600	Weak transcription	Right Ventricle	heart
35	chr7:140708400-140713800	Weak transcription	Ovary	ovary
36	chr7:140708600-140713400	Weak transcription	Primary B cells from cord blood	blood
37	chr7:140709800-140713600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr7:140710000-140713200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:140710000-140713200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr7:140710400-140713000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:140710400-140713000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:140710400-140713000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:140710400-140713200	Weak transcription	Fetal Brain Female	brain
44	chr7:140710400-140713400	Weak transcription	Adipose Nuclei	Adipose
45	chr7:140710400-140713400	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:140710400-140713400	Weak transcription	Fetal Stomach	stomach
47	chr7:140710400-140713600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr7:140710400-140713600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr7:140710400-140713600	Enhancers	Fetal Intestine Small	intestine
50	chr7:140710400-140713600	Weak transcription	Monocytes-CD14+_RO01746	blood

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