Variant report

Variant	rs3924962
Chromosome Location	chr7:140075999-140076000
allele	A/C
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	NFE2	chr7:140075993-140076056	GM12878	blood:	n/a	n/a
2	BCLAF1	chr7:140075992-140076417	GM12878	blood:	n/a	chr7:140076252-140076259

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140075069..140077735-chr7:140096588..140099526,2	MCF-7	breast:
2	chr7:140075072..140077306-chr7:140082163..140084967,2	K562	blood:

Variant related genes	Relation type
ENSG00000238868	TF binding region
ENSG00000157800	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10258709	0.89[EUR][1000 genomes]
rs12665885	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12667471	1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs12671831	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12673021	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12703771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12703772	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12703774	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12703775	0.85[EUR][1000 genomes]
rs12703777	0.87[EUR][1000 genomes]
rs12703778	0.87[EUR][1000 genomes]
rs12703782	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12703783	0.87[EUR][1000 genomes]
rs12703792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12703794	0.93[ASN][1000 genomes]
rs12703795	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12703797	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13232870	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13233309	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13244256	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4725685	0.89[EUR][1000 genomes]
rs4726780	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62490396	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6953981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6957189	0.88[EUR][1000 genomes]
rs6967815	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs7777207	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7778099	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7792038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9691058	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9692001	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3924962	CREB3L2	cis	parietal	SCAN
rs3924962	PARP12	cis	parietal	SCAN
rs3924962	OR9A2	cis	cerebellum	SCAN
rs3924962	MGAM	cis	parietal	SCAN
rs3924962	ZC3HAV1L	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
3	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
4	chr7:140046000-140076200	Weak transcription	Right Ventricle	heart
5	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
6	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:140049600-140076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
11	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
12	chr7:140051600-140076400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
15	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
17	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:140055600-140079200	Weak transcription	Fetal Kidney	kidney
19	chr7:140056800-140077400	Weak transcription	NH-A	brain
20	chr7:140056800-140079400	Weak transcription	Colonic Mucosa	Colon
21	chr7:140058600-140077800	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
23	chr7:140058800-140077800	Weak transcription	Placenta	Placenta
24	chr7:140058800-140079200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:140058800-140081400	Weak transcription	A549	lung
26	chr7:140058800-140084400	Weak transcription	Gastric	stomach
27	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
28	chr7:140059400-140091400	Weak transcription	Fetal Heart	heart
29	chr7:140061000-140076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:140063400-140082600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr7:140065000-140077000	Weak transcription	HMEC	breast
32	chr7:140065000-140077800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:140065200-140079200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:140066600-140077800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:140067800-140077800	Weak transcription	HSMMtube	muscle
36	chr7:140068000-140089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:140068200-140076800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr7:140068400-140078800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:140069000-140076000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:140069000-140077400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:140069000-140077800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr7:140069000-140077800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:140069000-140078400	Weak transcription	Spleen	Spleen
44	chr7:140069200-140076400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:140069200-140077800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr7:140069200-140077800	Weak transcription	Left Ventricle	heart
47	chr7:140069200-140082000	Weak transcription	Colon Smooth Muscle	Colon
48	chr7:140069400-140077800	Weak transcription	Ovary	ovary
49	chr7:140069400-140079200	Weak transcription	Brain Germinal Matrix	brain
50	chr7:140069600-140076400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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