Variant report

Variant	rs379462
Chromosome Location	chr3:52004317-52004318
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	chr3:52004060-52004555	K562	blood:	n/a	n/a
2	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52003390-52005696	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:52004247-52004620	K562	blood:	n/a	n/a
5	POLR2A	chr3:52004293-52005855	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52001556..52005448-chr3:52028528..52032420,5	MCF-7	breast:
2	chr3:51976428..51980212-chr3:52001978..52006587,6	MCF-7	breast:
3	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:

Variant related genes	Relation type
ABHD14A	TF binding region
PCBP4	TF binding region
ABHD14A-ACY1	TF binding region
ACY1	TF binding region
ENSG00000162244	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000114767	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11916396	1.00[ASN][1000 genomes]
rs11926611	0.84[YRI][hapmap]
rs2015691	0.92[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	0.92[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323861	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323862	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323863	0.85[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap]
rs323865	1.00[CHD][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[CHD][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs323868	1.00[MEX][hapmap]
rs323871	0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs323873	0.86[ASW][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs323874	0.86[ASW][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs323879	1.00[MEX][hapmap];0.83[YRI][hapmap]
rs323887	1.00[MEX][hapmap]
rs323890	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	0.92[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323893	0.86[ASW][hapmap];0.88[YRI][hapmap]
rs323894	0.83[AFR][1000 genomes]
rs323895	0.86[ASW][hapmap];0.88[YRI][hapmap]
rs323897	0.92[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323898	1.00[MEX][hapmap]
rs380788	0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs433823	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs72964028	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7432986	0.85[ASW][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes]
rs9840336	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs379462	ENSG00000114779	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52001800-52007600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52002000-52005800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:52002200-52007400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:52002400-52004400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:52002400-52004400	Enhancers	Brain Substantia Nigra	brain
6	chr3:52002400-52004600	Enhancers	Stomach Mucosa	stomach
7	chr3:52002400-52004800	Weak transcription	HMEC	breast
8	chr3:52002400-52005000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:52002400-52005000	Enhancers	Fetal Brain Male	brain
10	chr3:52002400-52005400	Enhancers	Pancreas	Pancrea
11	chr3:52002400-52005800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:52002400-52007200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:52002400-52007200	Enhancers	Liver	Liver
14	chr3:52002400-52007400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:52002400-52007400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:52002400-52007400	Weak transcription	Ovary	ovary
17	chr3:52002400-52007400	Weak transcription	Psoas Muscle	Psoas
18	chr3:52002400-52007400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:52002400-52007400	Weak transcription	NHDF-Ad	bronchial
20	chr3:52002400-52007600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:52002400-52007600	Weak transcription	Left Ventricle	heart
22	chr3:52002600-52004400	Enhancers	Brain Germinal Matrix	brain
23	chr3:52002600-52005600	Enhancers	Thymus	Thymus
24	chr3:52002600-52005800	Genic enhancers	Fetal Intestine Small	intestine
25	chr3:52002600-52007400	Weak transcription	Primary B cells from cord blood	blood
26	chr3:52002600-52007400	Weak transcription	Right Atrium	heart
27	chr3:52002800-52004400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:52002800-52004400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:52002800-52004400	Weak transcription	NHEK	skin
30	chr3:52002800-52004800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:52002800-52004800	Weak transcription	Lung	lung
32	chr3:52002800-52005000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:52002800-52006000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:52002800-52006800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:52002800-52006800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:52002800-52007000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:52002800-52007400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:52002800-52007400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:52002800-52007400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:52002800-52007400	Weak transcription	Colonic Mucosa	Colon
41	chr3:52002800-52007400	Weak transcription	GM12878-XiMat	blood
42	chr3:52002800-52007400	Weak transcription	HUVEC	blood vessel
43	chr3:52002800-52007400	Weak transcription	Osteobl	bone
44	chr3:52003000-52004400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:52003000-52004400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr3:52003000-52004600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:52003000-52004800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:52003000-52004800	Weak transcription	Right Ventricle	heart
49	chr3:52003000-52004800	Weak transcription	K562	blood
50	chr3:52003000-52004800	Weak transcription	NH-A	brain

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