Variant report

Variant	rs17012291
Chromosome Location	chr4:87970205-87970206
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	chr4:87967171-87970425	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87969741..87972043-chr4:88141021..88142542,2	MCF-7	breast:
2	chr4:87927007..87928738-chr4:87968800..87971824,3	K562	blood:
3	chr4:87965831..87967908-chr4:87968487..87970739,2	MCF-7	breast:
4	chr4:87854791..87857074-chr4:87968149..87971029,2	K562	blood:

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10022960	0.89[ASN][1000 genomes]
rs1374936	0.80[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs168161	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2053774	0.88[ASN][1000 genomes]
rs2272777	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.80[ASN][1000 genomes]
rs340627	1.00[ASN][1000 genomes]
rs340628	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340629	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340632	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340635	0.97[ASN][1000 genomes]
rs340640	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340644	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340646	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340649	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4536897	0.82[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4693155	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs4693799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58317309	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531943	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531944	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531945	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs6848056	0.90[ASN][1000 genomes]
rs6853011	0.89[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs895740	0.80[ASN][1000 genomes]
rs965824	0.91[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17012291	Hs.480174	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87960400-87975400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
3	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
5	chr4:87964800-87979200	Weak transcription	A549	lung
6	chr4:87966200-87979200	Weak transcription	NH-A	brain
7	chr4:87967000-87970600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:87967000-87971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:87967000-87975000	Strong transcription	Dnd41	blood
10	chr4:87967200-87971200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr4:87967400-87970800	Strong transcription	Fetal Thymus	thymus
12	chr4:87967400-87973000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr4:87967600-87971000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:87967600-87975000	Weak transcription	Stomach Mucosa	stomach
15	chr4:87967800-87970400	Strong transcription	HepG2	liver
16	chr4:87967800-87972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:87967800-87973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:87967800-87974600	Strong transcription	Fetal Intestine Large	intestine
19	chr4:87968200-87970400	Strong transcription	HUVEC	blood vessel
20	chr4:87968200-87970600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:87968200-87971000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
22	chr4:87968200-87971200	Strong transcription	Primary B cells from cord blood	blood
23	chr4:87968200-87971400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:87968400-87970600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:87968600-87970800	Strong transcription	Placenta	Placenta
26	chr4:87968600-87971800	Weak transcription	Aorta	Aorta
27	chr4:87968600-87971800	Weak transcription	Colonic Mucosa	Colon
28	chr4:87968600-87971800	Weak transcription	Right Atrium	heart
29	chr4:87968600-87974400	Enhancers	Colon Smooth Muscle	Colon
30	chr4:87968600-87975400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:87968600-87979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:87968800-87970400	Weak transcription	Thymus	Thymus
33	chr4:87968800-87970600	Weak transcription	Adipose Nuclei	Adipose
34	chr4:87968800-87970800	Weak transcription	Psoas Muscle	Psoas
35	chr4:87968800-87971200	Weak transcription	Ovary	ovary
36	chr4:87968800-87971800	Weak transcription	Fetal Stomach	stomach
37	chr4:87968800-87972000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:87968800-87972000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:87968800-87972000	Weak transcription	Pancreas	Pancrea
40	chr4:87968800-87973200	Weak transcription	Lung	lung
41	chr4:87968800-87973800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:87968800-87973800	Weak transcription	Small Intestine	intestine
43	chr4:87968800-87975000	Weak transcription	Gastric	stomach
44	chr4:87968800-87975400	Weak transcription	Spleen	Spleen
45	chr4:87968800-87975600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:87968800-87975800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:87968800-87975800	Weak transcription	NHEK	skin
48	chr4:87968800-87975800	Weak transcription	NHLF	lung
49	chr4:87968800-87976200	Weak transcription	NHDF-Ad	bronchial
50	chr4:87968800-87977600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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