Variant report

Variant	rs6946840
Chromosome Location	chr7:3342722-3342723
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	TCF7L2	chr7:3342190-3343032	HEK293	kidney:	n/a	n/a
2	RAD21	chr7:3341429-3344236	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3342709..3344229-chr7:3346065..3349002,2	K562	blood:

Variant related genes	Relation type
ENSG00000236708	TF binding region

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs11972733	1.00[ASN][1000 genomes]
rs11973104	1.00[ASN][1000 genomes]
rs11973436	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973741	1.00[ASN][1000 genomes]
rs11973959	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974237	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974565	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11975595	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978310	1.00[ASN][1000 genomes]
rs11979270	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981004	1.00[ASN][1000 genomes]
rs11981125	1.00[ASN][1000 genomes]
rs11981207	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981998	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982674	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983341	1.00[ASN][1000 genomes]
rs12700786	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700790	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700791	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236105	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404872	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522503	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133260	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133277	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133284	1.00[ASN][1000 genomes]
rs17133303	1.00[ASN][1000 genomes]
rs17133309	1.00[ASN][1000 genomes]
rs17133324	1.00[ASN][1000 genomes]
rs17741019	1.00[ASN][1000 genomes]
rs1961404	0.81[EUR][1000 genomes]
rs2334059	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34431029	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34466031	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34727194	1.00[ASN][1000 genomes]
rs35298757	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268017	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4358699	1.00[ASN][1000 genomes]
rs4428572	1.00[ASN][1000 genomes]
rs4509207	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560699	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55944002	1.00[ASN][1000 genomes]
rs56064609	0.82[EUR][1000 genomes]
rs56138263	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56193850	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56217543	1.00[ASN][1000 genomes]
rs57427044	0.81[EUR][1000 genomes]
rs57534358	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57535226	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57585396	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58338081	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59021191	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59076306	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59296189	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59478367	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59673826	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60243572	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60418263	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60682391	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61039995	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61401313	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492969	1.00[ASN][1000 genomes]
rs66546301	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66665337	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66941572	1.00[ASN][1000 genomes]
rs67447866	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67461903	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67498702	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67637487	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67691723	1.00[ASN][1000 genomes]
rs67924867	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68115111	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68165343	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942774	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943523	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6944617	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944745	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945914	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948557	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952184	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955021	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959134	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962043	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963043	1.00[ASN][1000 genomes]
rs6964818	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6969044	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969455	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974121	1.00[ASN][1000 genomes]
rs6977110	1.00[ASN][1000 genomes]
rs6977532	0.86[EUR][1000 genomes]
rs73034713	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034779	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036706	1.00[ASN][1000 genomes]
rs73045613	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73045637	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73045677	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73046618	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73046656	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046658	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046661	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046682	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046689	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046694	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046699	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046702	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048614	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048617	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73048621	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048624	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048628	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048630	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048631	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048634	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048643	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048645	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048648	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048655	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048661	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048668	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048672	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048676	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048677	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048700	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73049436	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73049438	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73050503	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050538	1.00[ASN][1000 genomes]
rs73050542	1.00[ASN][1000 genomes]
rs73052642	1.00[ASN][1000 genomes]
rs7779193	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782339	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783541	0.86[EUR][1000 genomes]
rs7785207	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792929	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807563	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808804	0.81[EUR][1000 genomes]
rs9771086	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3340000-3343400	Active TSS	Aorta	Aorta
2	chr7:3340200-3342800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:3340200-3343000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr7:3340200-3343200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:3340400-3342800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr7:3340400-3343000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:3341400-3342800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr7:3341400-3342800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr7:3341600-3342800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr7:3341600-3342800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
11	chr7:3341600-3342800	Bivalent/Poised TSS	NHDF-Ad	bronchial
12	chr7:3342200-3342800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:3342200-3342800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:3342200-3343200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:3342200-3344600	Weak transcription	Psoas Muscle	Psoas
16	chr7:3342400-3343800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:3342400-3344000	Weak transcription	Pancreas	Pancrea
18	chr7:3342600-3342800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr7:3342600-3342800	Active TSS	Adipose Nuclei	Adipose
20	chr7:3342600-3342800	Active TSS	Fetal Brain Female	brain
21	chr7:3342600-3342800	Enhancers	Fetal Lung	lung
22	chr7:3342600-3342800	Active TSS	Stomach Smooth Muscle	stomach
23	chr7:3342600-3343000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr7:3342600-3343000	Enhancers	Fetal Heart	heart
25	chr7:3342600-3343000	Enhancers	Rectal Smooth Muscle	rectum
26	chr7:3342600-3343400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:3342600-3343600	Weak transcription	HepG2	liver
28	chr7:3342600-3344200	Enhancers	Colon Smooth Muscle	Colon
29	chr7:3342600-3344600	Weak transcription	Fetal Brain Male	brain
30	chr7:3342600-3347200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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