Variant report

Variant	rs12374317
Chromosome Location	chr4:713920-713921
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:713177..716700-chr4:718880..722359,3	MCF-7	breast:
2	chr4:713342..715491-chr4:723785..726494,2	K562	blood:
3	chr4:706713..710070-chr4:713256..715563,3	K562	blood:
4	chr4:707355..710100-chr4:713683..715798,2	MCF-7	breast:
5	chr4:665538..669787-chr4:710811..715751,5	MCF-7	breast:
6	chr4:696628..698929-chr4:713327..715075,2	MCF-7	breast:
7	chr4:713856..715450-chr4:749624..752422,2	K562	blood:
8	chr4:700678..704217-chr4:710705..714201,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169020	Chromatin interaction
ENSG00000215375	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000272588	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10004172	0.81[ASN][1000 genomes]
rs11248035	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11248036	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728488	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11734460	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11735280	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11940788	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12374324	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12502944	0.81[ASN][1000 genomes]
rs12504026	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505220	0.81[ASN][1000 genomes]
rs17164964	0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs4234853	0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs4690186	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4690187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4690188	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4690189	0.81[ASN][1000 genomes]
rs4690292	0.90[CEU][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4690293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4690294	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4690295	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55990625	0.81[ASN][1000 genomes]
rs73221103	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73221121	0.81[ASN][1000 genomes]
rs73221124	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv870115	chr4:692811-733794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	esv1833383	chr4:708887-753697	Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv878253	chr4:708932-771587	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
17	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv593210	chr4:712222-725867	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv878256	chr4:712222-744098	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
22	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
23	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
24	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12374317	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:701200-714600	Weak transcription	NHDF-Ad	bronchial
2	chr4:701200-724400	Weak transcription	Aorta	Aorta
3	chr4:701400-714000	Weak transcription	HMEC	breast
4	chr4:701400-715200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:701400-724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:701400-724800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:701600-716800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:702200-754800	Weak transcription	Hela-S3	cervix
9	chr4:702400-714600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:702400-720000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:702400-720200	Weak transcription	NH-A	brain
12	chr4:702600-715800	Weak transcription	Liver	Liver
13	chr4:702600-716800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:702600-724400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:702800-714600	Weak transcription	Stomach Mucosa	stomach
16	chr4:702800-715000	Weak transcription	GM12878-XiMat	blood
17	chr4:702800-726600	Weak transcription	Primary B cells from cord blood	blood
18	chr4:703000-714000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:703000-714000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:703000-716600	Weak transcription	Fetal Lung	lung
21	chr4:703400-714400	Weak transcription	Primary T cells from cord blood	blood
22	chr4:703400-714800	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:703400-717800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:703400-724800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:703400-726800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:703600-714600	Weak transcription	HUVEC	blood vessel
27	chr4:703600-727200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:703800-715400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:703800-724400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:704000-724400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:704200-714600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:704200-715800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:704400-714400	Weak transcription	HSMM	muscle
34	chr4:704400-714600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:704400-714600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:704400-714600	Weak transcription	Right Atrium	heart
37	chr4:704400-715600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:704400-721200	Weak transcription	Small Intestine	intestine
39	chr4:704400-721400	Weak transcription	A549	lung
40	chr4:704600-714200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:704600-727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:704800-714400	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:704800-714600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:704800-714600	Weak transcription	Brain Angular Gyrus	brain
45	chr4:704800-714800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:704800-724600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:705000-714000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:705000-714800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr4:705000-715400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:705000-724400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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