Variant report

Variant	rs6965394
Chromosome Location	chr7:22233674-22233675
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	SIN3A	chr7:22232869-22233694	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr7:22233248-22233675	H1-hESC	embryonic stem cell:	n/a	n/a
3	YY1	chr7:22233069-22233681	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr7:22232778-22233701	H1-neurons	neurons:	n/a	n/a
5	ATF2	chr7:22233182-22233687	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr7:22233215-22233678	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr7:22233270-22233700	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr7:22232727-22233822	H1-neurons	neurons:	n/a	n/a
9	MAX	chr7:22233240-22233759	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr7:22233223-22233751	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr7:22232395-22233767	H1-neurons	neurons:	n/a	n/a
12	JUND	chr7:22233064-22233726	H1-hESC	embryonic stem cell:	n/a	n/a
13	SP1	chr7:22233213-22233707	H1-hESC	embryonic stem cell:	n/a	chr7:22233417-22233428
14	TEAD4	chr7:22233264-22233688	H1-hESC	embryonic stem cell:	n/a	n/a
15	SP1	chr7:22233208-22233783	H1-hESC	embryonic stem cell:	n/a	chr7:22233417-22233428
16	YY1	chr7:22233163-22233688	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr7:22231867-22233981	H1-neurons	neurons:	n/a	n/a
18	CTBP2	chr7:22232964-22233814	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD2	chr7:22233228-22233683	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr7:22232392-22233752	H1-neurons	neurons:	n/a	n/a
21	RAD21	chr7:22233068-22233715	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr7:22232742-22233779	H1-neurons	neurons:	n/a	n/a
23	ZNF143	chr7:22233230-22233698	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RAPGEF5	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10250341	1.00[CHB][hapmap]
rs10250355	1.00[CHB][hapmap]
rs10255486	1.00[CHB][hapmap]
rs10282106	0.88[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282222	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950895	1.00[CHB][hapmap];0.91[MKK][hapmap]
rs11763898	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12530484	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533150	1.00[CHB][hapmap]
rs1345251	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17146362	1.00[ASW][hapmap]
rs17773555	0.86[CEU][hapmap]
rs17774699	1.00[ASW][hapmap]
rs2079478	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813383	0.86[TSI][hapmap]
rs4291165	1.00[CHB][hapmap]
rs4496855	1.00[CHB][hapmap]
rs4590334	1.00[CHB][hapmap]
rs4640962	1.00[CHB][hapmap]
rs4722108	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722110	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5014150	1.00[CHB][hapmap];0.92[AFR][1000 genomes]
rs6461640	1.00[CHB][hapmap];0.91[MKK][hapmap]
rs6461641	1.00[CHB][hapmap]
rs6944433	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948973	1.00[CHB][hapmap]
rs6949461	1.00[CHB][hapmap]
rs6960229	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971344	1.00[CHB][hapmap]
rs6980127	1.00[CHB][hapmap]
rs73683318	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796738	1.00[CHB][hapmap]
rs7809342	1.00[CHB][hapmap];0.91[MKK][hapmap]
rs7810806	0.89[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9886139	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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	nsv606405	chr7:22202485-22235825	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:22184600-22240600	Weak transcription	Colonic Mucosa	Colon
2	chr7:22214400-22247400	Weak transcription	HUVEC	blood vessel
3	chr7:22219600-22234600	Weak transcription	Primary T cells from cord blood	blood
4	chr7:22222200-22235200	Weak transcription	GM12878-XiMat	blood
5	chr7:22223200-22242600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:22223800-22234200	Weak transcription	HMEC	breast
7	chr7:22225400-22253600	Weak transcription	Stomach Mucosa	stomach
8	chr7:22225800-22246800	Strong transcription	Dnd41	blood
9	chr7:22227000-22236800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr7:22227400-22245600	Strong transcription	HepG2	liver
11	chr7:22228000-22233800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr7:22228800-22233800	Active TSS	Brain Angular Gyrus	brain
13	chr7:22228800-22233800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:22229200-22233800	Active TSS	Brain Cingulate Gyrus	brain
15	chr7:22229200-22233800	Active TSS	Brain Substantia Nigra	brain
16	chr7:22229600-22233800	Strong transcription	Liver	Liver
17	chr7:22230400-22243000	Weak transcription	Gastric	stomach
18	chr7:22232000-22233800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr7:22232400-22234600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:22232600-22233800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:22232600-22233800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
22	chr7:22232600-22233800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr7:22232800-22233800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:22232800-22233800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:22232800-22233800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:22232800-22233800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:22232800-22233800	Active TSS	Osteobl	bone
28	chr7:22233000-22233800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr7:22233000-22233800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:22233000-22233800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr7:22233000-22233800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:22233000-22233800	Active TSS	Fetal Kidney	kidney
33	chr7:22233000-22235400	Weak transcription	Primary B cells from cord blood	blood
34	chr7:22233200-22233800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:22233200-22233800	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr7:22233400-22233800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr7:22233400-22233800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:22233400-22233800	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr7:22233400-22233800	Flanking Active TSS	Fetal Brain Male	brain
40	chr7:22233400-22233800	Flanking Active TSS	Fetal Brain Female	brain
41	chr7:22233400-22234200	Weak transcription	Fetal Thymus	thymus
42	chr7:22233400-22234400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr7:22233400-22235400	Strong transcription	Fetal Intestine Large	intestine
44	chr7:22233400-22247600	Weak transcription	Psoas Muscle	Psoas
45	chr7:22233400-22259200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:22233600-22233800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr7:22233600-22233800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr7:22233600-22233800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr7:22233600-22233800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:22233600-22233800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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