Variant report

Variant	rs678354
Chromosome Location	chr3:101573052-101573053
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:101572198-101573053	K562	blood:	n/a	n/a
2	POLR2A	chr3:101567198-101574916	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:101565720-101574900	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:101567627-101574860	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:101571512-101574724	GM18505	blood:	n/a	n/a
6	POLR2A	chr3:101571647-101574739	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:101572992-101573141	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:101572974-101573099	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:101572033-101573146	K562	blood:	n/a	n/a
10	POLR2A	chr3:101572898-101573082	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:101569085-101574846	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:101571603-101573176	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:101567553-101574820	IMR90	lung:	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	chr3:101571698-101573214	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:101571658-101574759	A549	lung:	n/a	n/a
18	POLR2A	chr3:101571676-101574197	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr3:101567371-101573695	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr3:101572901-101573152	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:101567162-101574755	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr3:101571710-101573147	GM12891	blood:	n/a	n/a
23	POLR2A	chr3:101568040-101574948	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:101571666-101573228	GM12891	blood:	n/a	n/a
25	POLR2A	chr3:101572166-101573390	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr3:101567611-101574981	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101570369..101573097-chr3:101618307..101620488,2	MCF-7	breast:
2	chr3:101543661..101554550-chr3:101566310..101574179,30	MCF-7	breast:

No data

Variant related genes	Relation type
NFKBIZ	TF binding region
ENSG00000249474	Chromatin interaction
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs14134	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs2925332	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2925333	0.80[ASN][1000 genomes]
rs2926539	0.93[ASW][hapmap];0.83[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2926540	0.83[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs587555	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592332	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs592779	0.86[ASW][hapmap];0.83[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs599849	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs601225	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617688	0.81[CHD][hapmap]
rs618901	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs622122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs654219	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs665374	0.83[CEU][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs677011	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	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs681573	0.86[ASW][hapmap];0.83[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs688058	0.93[ASW][hapmap];0.82[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs694293	0.83[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101569200-101573600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:101569800-101576400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:101570000-101574400	Weak transcription	Fetal Brain Female	brain
4	chr3:101570000-101578000	Weak transcription	Brain Germinal Matrix	brain
5	chr3:101570000-101579200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:101570200-101574800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
7	chr3:101570400-101574800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:101570600-101573200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
10	chr3:101570600-101573200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
11	chr3:101570600-101574200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr3:101570600-101577600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
13	chr3:101570800-101576600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
14	chr3:101570800-101579400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:101570800-101580600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr3:101570800-101580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:101570800-101580800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:101570800-101580800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:101571000-101574200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
20	chr3:101571000-101574400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:101571000-101574800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr3:101571000-101574800	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
23	chr3:101571000-101575000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:101571000-101576000	Strong transcription	Brain Anterior Caudate	brain
25	chr3:101571000-101576800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:101571000-101577200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:101571000-101579400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr3:101571000-101579400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:101571000-101579400	Strong transcription	Dnd41	blood
30	chr3:101571000-101580000	Strong transcription	Fetal Lung	lung
31	chr3:101571000-101580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:101571000-101581400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:101571200-101574200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr3:101571200-101574400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:101571200-101575000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:101571200-101575800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr3:101571200-101576200	Strong transcription	Brain Substantia Nigra	brain
38	chr3:101571200-101576600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:101571200-101576600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr3:101571200-101576600	Strong transcription	Ovary	ovary
41	chr3:101571200-101579400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:101571200-101579400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:101571200-101579400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:101571200-101579400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:101571200-101579400	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:101571200-101580600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:101571200-101580600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:101571200-101581000	Strong transcription	Colon Smooth Muscle	Colon
49	chr3:101571200-101582000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:101571400-101573600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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