Variant report

Variant	rs17604480
Chromosome Location	chr4:87970127-87970128
allele	A/C
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: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10516788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471251	0.98[ASN][1000 genomes]
rs17012234	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17012334	0.82[EUR][1000 genomes]
rs17701999	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17752307	0.80[ASN][1000 genomes]
rs2061498	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4693801	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55787557	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55816619	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55879154	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55913164	0.80[ASN][1000 genomes]
rs55982755	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56023922	0.82[ASN][1000 genomes]
rs56050898	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56201818	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56390363	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56395939	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56406125	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6819155	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840258	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6854749	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667747	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667748	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667751	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667752	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667753	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667754	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667757	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72667759	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72667765	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665282	0.80[ASN][1000 genomes]
rs767315	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682652	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695426	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];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

No data

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	chr4:87967400-87970200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:87967400-87970800	Strong transcription	Fetal Thymus	thymus
13	chr4:87967400-87973000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr4:87967600-87970200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:87967600-87970200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:87967600-87971000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:87967600-87975000	Weak transcription	Stomach Mucosa	stomach
18	chr4:87967800-87970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:87967800-87970200	Strong transcription	Fetal Lung	lung
20	chr4:87967800-87970400	Strong transcription	HepG2	liver
21	chr4:87967800-87972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:87967800-87973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:87967800-87974600	Strong transcription	Fetal Intestine Large	intestine
24	chr4:87968200-87970200	Strong transcription	Osteobl	bone
25	chr4:87968200-87970400	Strong transcription	HUVEC	blood vessel
26	chr4:87968200-87970600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:87968200-87971000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:87968200-87971200	Strong transcription	Primary B cells from cord blood	blood
29	chr4:87968200-87971400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:87968400-87970600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:87968600-87970800	Strong transcription	Placenta	Placenta
32	chr4:87968600-87971800	Weak transcription	Aorta	Aorta
33	chr4:87968600-87971800	Weak transcription	Colonic Mucosa	Colon
34	chr4:87968600-87971800	Weak transcription	Right Atrium	heart
35	chr4:87968600-87974400	Enhancers	Colon Smooth Muscle	Colon
36	chr4:87968600-87975400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:87968600-87979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:87968800-87970400	Weak transcription	Thymus	Thymus
39	chr4:87968800-87970600	Weak transcription	Adipose Nuclei	Adipose
40	chr4:87968800-87970800	Weak transcription	Psoas Muscle	Psoas
41	chr4:87968800-87971200	Weak transcription	Ovary	ovary
42	chr4:87968800-87971800	Weak transcription	Fetal Stomach	stomach
43	chr4:87968800-87972000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:87968800-87972000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:87968800-87972000	Weak transcription	Pancreas	Pancrea
46	chr4:87968800-87973200	Weak transcription	Lung	lung
47	chr4:87968800-87973800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:87968800-87973800	Weak transcription	Small Intestine	intestine
49	chr4:87968800-87975000	Weak transcription	Gastric	stomach
50	chr4:87968800-87975400	Weak transcription	Spleen	Spleen

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