Variant report

Variant	rs677011
Chromosome Location	chr3:101574503-101574504
allele	A/G
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	POLR2A	chr3:101573703-101574747	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:101567198-101574916	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:101574485-101574608	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:101574417-101574676	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:101565720-101574900	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:101567627-101574860	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:101571512-101574724	GM18505	blood:	n/a	n/a
8	POLR2A	chr3:101571647-101574739	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:101569085-101574846	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:101567553-101574820	IMR90	lung:	n/a	n/a
11	POLR2A	chr3:101574435-101574509	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:101573833-101574650	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:101574366-101574872	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:101567615-101574974	SK-N-SH	brain:	n/a	n/a
15	CHD1	chr3:101568171-101574913	IMR90	lung:	n/a	n/a
16	POLR2A	chr3:101573349-101574985	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:101573255-101574738	GM12892	blood:	n/a	n/a
18	POLR2A	chr3:101571658-101574759	A549	lung:	n/a	n/a
19	POLR2A	chr3:101574366-101574816	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:101567162-101574755	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:101568040-101574948	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:101574221-101574778	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:101567611-101574981	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:101574311-101574782	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
NFKBIZ	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs14134	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2925332	0.82[ASN][1000 genomes]
rs2925333	0.80[ASN][1000 genomes]
rs2926539	0.84[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs2926540	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs587555	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592332	0.82[ASN][1000 genomes]
rs592779	0.84[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs599849	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs601225	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617688	0.81[CHD][hapmap]
rs618901	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs622122	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654219	0.82[ASN][1000 genomes]
rs665374	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs678354	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680508	0.92[ASN][1000 genomes]
rs681573	0.84[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs688058	0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs694293	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs694936	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs677011	TOMM70A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101569800-101576400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:101570000-101578000	Weak transcription	Brain Germinal Matrix	brain
3	chr3:101570000-101579200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:101570200-101574800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
5	chr3:101570400-101574800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
6	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:101570600-101577600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
8	chr3:101570800-101576600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
9	chr3:101570800-101579400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:101570800-101580600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr3:101570800-101580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:101570800-101580800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:101570800-101580800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:101571000-101574800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:101571000-101574800	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
16	chr3:101571000-101575000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:101571000-101576000	Strong transcription	Brain Anterior Caudate	brain
18	chr3:101571000-101576800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:101571000-101577200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:101571000-101579400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr3:101571000-101579400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:101571000-101579400	Strong transcription	Dnd41	blood
23	chr3:101571000-101580000	Strong transcription	Fetal Lung	lung
24	chr3:101571000-101580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:101571000-101581400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:101571200-101575000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:101571200-101575800	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr3:101571200-101576200	Strong transcription	Brain Substantia Nigra	brain
29	chr3:101571200-101576600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:101571200-101576600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:101571200-101576600	Strong transcription	Ovary	ovary
32	chr3:101571200-101579400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:101571200-101579400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:101571200-101579400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:101571200-101579400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr3:101571200-101579400	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:101571200-101580600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:101571200-101580600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:101571200-101581000	Strong transcription	Colon Smooth Muscle	Colon
40	chr3:101571200-101582000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:101571400-101574600	Genic enhancers	Pancreas	Pancrea
42	chr3:101571400-101574600	Genic enhancers	Stomach Mucosa	stomach
43	chr3:101571400-101574800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr3:101571400-101574800	Strong transcription	Hela-S3	cervix
45	chr3:101571400-101575000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:101571400-101575000	Strong transcription	Brain Hippocampus Middle	brain
47	chr3:101571400-101576000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:101571400-101576600	Strong transcription	Fetal Stomach	stomach
49	chr3:101571400-101579600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:101571400-101580800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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