Variant report

Variant	rs17012739
Chromosome Location	chr4:128814964-128814965
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128807809..128810684-chr4:128813314..128816691,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142731	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10024450	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10493147	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1064205	1.00[CEU][hapmap];0.80[GIH][hapmap]
rs10857126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098936	0.84[CEU][hapmap]
rs11098937	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap]
rs11098940	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11098947	0.92[CEU][hapmap]
rs11725843	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12503257	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504266	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12504825	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506549	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs12510785	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12511932	0.84[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs12641548	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs12645068	0.84[EUR][1000 genomes]
rs12645636	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs13122568	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap]
rs13127610	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap]
rs1380154	0.80[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1380156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1459048	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1459049	0.83[CHB][hapmap]
rs1459050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1585312	0.84[CEU][hapmap]
rs16997980	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs1870422	0.92[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs1903104	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs1975878	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs1975879	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs1993722	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs2085655	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2305957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305958	0.84[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2306054	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs3214038	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs3775982	0.82[CEU][hapmap]
rs3811740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811741	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3816588	0.86[CEU][hapmap];0.84[YRI][hapmap]
rs4435753	0.84[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs4833383	0.83[CHB][hapmap]
rs4833391	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4833393	0.81[EUR][1000 genomes]
rs4834214	0.83[GIH][hapmap]
rs4834217	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs4834223	0.88[CEU][hapmap]
rs4834224	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs4834225	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs4834226	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs4834229	1.00[CEU][hapmap]
rs55798529	0.86[EUR][1000 genomes]
rs62335590	0.82[EUR][1000 genomes]
rs6534638	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6534647	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6534648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6534656	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6534659	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs6821748	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6839292	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6846535	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7376138	0.84[EUR][1000 genomes]
rs7441217	0.81[ASN][1000 genomes]
rs748630	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7654638	0.84[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs7671590	0.92[CEU][hapmap]
rs7684368	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7692740	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs769293	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs959822	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9968459	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9995738	0.84[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats 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	44 gene(s)	inside rSNPs	diseases
9	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv1019193	chr4:128810527-128949320	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17012739	HSPA4L	cis	cerebellum	SCAN
rs17012739	LARP1B	cis	parietal	SCAN
rs17012739	PLK4	cis	cerebellum	SCAN
rs17012739	C4orf29	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128802800-128815600	Weak transcription	Aorta	Aorta
2	chr4:128802800-128819200	Weak transcription	Left Ventricle	heart
3	chr4:128803000-128819400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:128803000-128820800	Weak transcription	Esophagus	oesophagus
5	chr4:128803000-128826200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:128803200-128815800	Weak transcription	Brain Anterior Caudate	brain
7	chr4:128803200-128816600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:128803200-128817000	Weak transcription	NHLF	lung
9	chr4:128803200-128818600	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:128803200-128819000	Weak transcription	Fetal Brain Male	brain
11	chr4:128803200-128819000	Weak transcription	Fetal Kidney	kidney
12	chr4:128803200-128819600	Weak transcription	Primary B cells from cord blood	blood
13	chr4:128803200-128820200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:128803200-128821200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:128803400-128820400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:128803400-128821200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:128803400-128822400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:128803400-128841800	Weak transcription	Brain Germinal Matrix	brain
19	chr4:128803600-128816400	Weak transcription	Fetal Heart	heart
20	chr4:128803600-128819600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:128803600-128820400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:128803600-128821200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:128804000-128818800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:128804000-128821000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:128804000-128821000	Strong transcription	Fetal Thymus	thymus
26	chr4:128804600-128820800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:128804800-128820600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:128805800-128821400	Weak transcription	Hela-S3	cervix
29	chr4:128807200-128819200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:128807200-128820800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:128807800-128816400	Weak transcription	Ovary	ovary
32	chr4:128807800-128817000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:128807800-128819800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:128808000-128817000	Weak transcription	Osteobl	bone
35	chr4:128808000-128817800	Weak transcription	Fetal Brain Female	brain
36	chr4:128808800-128815000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:128808800-128817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:128809200-128818800	Weak transcription	Fetal Intestine Small	intestine
39	chr4:128809200-128823000	Weak transcription	Fetal Stomach	stomach
40	chr4:128809400-128826200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:128809600-128816800	Weak transcription	Thymus	Thymus
42	chr4:128809800-128815000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:128810200-128819200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:128810400-128818200	Strong transcription	NH-A	brain
45	chr4:128810600-128820000	Strong transcription	HMEC	breast
46	chr4:128810800-128817000	Weak transcription	Brain Substantia Nigra	brain
47	chr4:128810800-128818800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:128810800-128819400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:128810800-128821200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:128811000-128815400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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