Variant report

Variant	rs1140034
Chromosome Location	chr7:140374049-140374050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr7:140372574-140374124	GM12878	blood:	n/a	chr7:140372797-140372809
2	EP300	chr7:140374046-140374386	GM12878	blood:	n/a	n/a
3	MTA3	chr7:140372943-140374693	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:140372379-140374681	Raji	blood:	n/a	n/a
5	RUNX3	chr7:140373846-140374567	GM12878	blood:	n/a	n/a
6	SPI1	chr7:140374029-140374797	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:140372510-140374150	GM19193	blood:	n/a	n/a
8	POLR2A	chr7:140373128-140374446	K562	blood:	n/a	n/a
9	ZNF263	chr7:140372859-140374131	HEK293-T-REx	kidney:	n/a	n/a
10	RELA	chr7:140373325-140374592	GM18951	blood:	n/a	n/a
11	RUNX3	chr7:140373975-140374390	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140372637..140375611-chr7:140394231..140397834,5	K562	blood:
2	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:
3	chr7:140372831..140374417-chr7:140400299..140402616,2	MCF-7	breast:
4	chr7:140371506..140376729-chr7:140377280..140380130,6	K562	blood:
5	chr7:140371560..140374067-chr7:140396511..140398663,2	K562	blood:
6	chr7:140371193..140374993-chr7:140376654..140380151,6	MCF-7	breast:
7	chr7:140177294..140179711-chr7:140373712..140375545,2	K562	blood:
8	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK2	TF binding region
DENND2A	TF binding region
ENSG00000090266	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000133606	Chromatin interaction
ENSG00000240889	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10228254	0.85[ASN][1000 genomes]
rs10241711	0.83[CHB][hapmap]
rs10258462	0.85[ASN][1000 genomes]
rs10258465	0.85[ASN][1000 genomes]
rs10260676	0.83[ASN][1000 genomes]
rs12375245	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1267600	0.91[CHB][hapmap]
rs1267601	0.91[CHB][hapmap]
rs1267606	0.91[CHB][hapmap]
rs1267611	0.81[CHB][hapmap]
rs1267613	0.81[CHB][hapmap]
rs1267619	0.91[CHB][hapmap]
rs1267636	0.81[CHB][hapmap]
rs1267638	0.91[CHB][hapmap]
rs1267642	0.81[CHB][hapmap]
rs1267643	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1267644	0.81[CHB][hapmap]
rs1267649	0.91[CHB][hapmap]
rs1639675	0.91[CHB][hapmap]
rs1639678	0.91[CHB][hapmap]
rs1639679	0.81[CHB][hapmap]
rs17161666	0.83[CHB][hapmap]
rs17161668	0.81[ASN][1000 genomes]
rs17161750	0.91[CHB][hapmap]
rs1733827	0.91[CHB][hapmap]
rs1733832	0.91[CHB][hapmap]
rs2364393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2364394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2364395	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364396	0.83[CHB][hapmap]
rs2364397	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs2364399	0.80[MKK][hapmap]
rs2535951	0.91[CHB][hapmap]
rs28517771	0.90[ASN][1000 genomes]
rs2907950	0.89[ASN][1000 genomes]
rs2930315	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930318	0.94[ASN][1000 genomes]
rs2930319	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2930328	0.89[MKK][hapmap]
rs2930329	0.89[MKK][hapmap]
rs2930331	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968549	0.87[ASN][1000 genomes]
rs2968550	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs2968551	0.92[ASN][1000 genomes]
rs2968553	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2968555	0.96[ASN][1000 genomes]
rs2968558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968559	0.94[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725799	0.81[ASN][1000 genomes]
rs4727011	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727021	0.81[ASN][1000 genomes]
rs4727036	0.81[ASN][1000 genomes]
rs4727040	0.83[CHB][hapmap]
rs4727041	0.83[CHB][hapmap]
rs6464036	0.91[CHB][hapmap]
rs6464123	0.91[CHB][hapmap]
rs6464937	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977834	0.87[ASN][1000 genomes]
rs73505645	0.90[ASN][1000 genomes]
rs73505647	0.88[ASN][1000 genomes]
rs7792746	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7794857	0.85[ASN][1000 genomes]
rs7803697	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.87[ASN][1000 genomes]
rs7809339	0.81[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	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1140034	NDUFB2	cis	lymphoblastoid	seeQTL
rs1140034	TMEM139	cis	parietal	SCAN
rs1140034	ADCK2	Cis_1M	lymphoblastoid	RTeQTL
rs1140034	DGKI	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140372400-140374400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:140372600-140375800	Enhancers	Fetal Brain Male	brain
3	chr7:140373000-140374200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr7:140373000-140374400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr7:140373000-140374600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr7:140373000-140375400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:140373200-140374200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr7:140373200-140374200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:140373200-140374200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr7:140373200-140374200	Flanking Active TSS	K562	blood
11	chr7:140373200-140374400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:140373200-140374400	Flanking Active TSS	Colonic Mucosa	Colon
13	chr7:140373200-140374400	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr7:140373200-140374400	Flanking Active TSS	HMEC	breast
15	chr7:140373200-140374600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:140373200-140374600	Flanking Active TSS	GM12878-XiMat	blood
17	chr7:140373200-140374800	Flanking Active TSS	Dnd41	blood
18	chr7:140373400-140374200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:140373400-140374200	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr7:140373400-140374200	Flanking Active TSS	Placenta	Placenta
21	chr7:140373400-140374200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr7:140373400-140374400	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr7:140373400-140374400	Flanking Active TSS	Fetal Brain Female	brain
24	chr7:140373400-140374600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:140373400-140374600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr7:140373400-140374800	Enhancers	Fetal Heart	heart
27	chr7:140373400-140383200	Weak transcription	HSMMtube	muscle
28	chr7:140373600-140374200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
29	chr7:140373600-140374200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr7:140373600-140374200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:140373600-140374200	Enhancers	Psoas Muscle	Psoas
32	chr7:140373600-140374200	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr7:140373600-140374400	Enhancers	Spleen	Spleen
34	chr7:140373600-140374600	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr7:140373600-140374600	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr7:140373600-140374600	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr7:140373600-140374600	Enhancers	Lung	lung
38	chr7:140373600-140374600	Enhancers	HUVEC	blood vessel
39	chr7:140373600-140374600	Flanking Active TSS	NHDF-Ad	bronchial
40	chr7:140373600-140374800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:140373600-140374800	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr7:140373600-140374800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr7:140373600-140375400	Enhancers	Hela-S3	cervix
44	chr7:140373600-140377800	Enhancers	Primary B cells from cord blood	blood
45	chr7:140373600-140385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:140373800-140374200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:140373800-140374200	Active TSS	Osteobl	bone
48	chr7:140373800-140374400	Enhancers	Primary hematopoietic stem cells	blood
49	chr7:140373800-140374400	Enhancers	Liver	Liver
50	chr7:140373800-140374400	Enhancers	Placenta Amnion	Placenta Amnion

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