Variant report

Variant	rs4687802
Chromosome Location	chr3:52111051-52111052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52108818..52113062-chr3:52113432..52117079,5	K562	blood:
2	chr3:52104770..52107611-chr3:52108518..52111344,2	K562	blood:
3	chr3:52089479..52092254-chr3:52110103..52112937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12485855	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12488456	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12489539	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493204	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051963	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821841	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687608	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4687609	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687801	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687806	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687808	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687809	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66530305	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72622937	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7618573	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920160	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9637473	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
2	chr3:52102000-52111200	Weak transcription	Fetal Kidney	kidney
3	chr3:52102600-52121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
6	chr3:52103400-52114600	Weak transcription	Fetal Intestine Large	intestine
7	chr3:52105600-52111200	Weak transcription	Osteobl	bone
8	chr3:52105600-52119600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:52105600-52120800	Strong transcription	Dnd41	blood
10	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
11	chr3:52105800-52112000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52105800-52119200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
14	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
15	chr3:52106000-52111400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:52106200-52121000	Weak transcription	HSMM	muscle
17	chr3:52106400-52112000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:52106400-52114400	Weak transcription	HMEC	breast
19	chr3:52106600-52111200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:52106800-52111200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:52107200-52123200	Weak transcription	Fetal Brain Female	brain
22	chr3:52107400-52113600	Strong transcription	Thymus	Thymus
23	chr3:52107600-52111600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:52107800-52111200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52108200-52114000	Weak transcription	K562	blood
26	chr3:52108400-52112800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:52108400-52113000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:52108800-52122200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52109000-52111200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:52109200-52113200	Enhancers	Fetal Muscle Leg	muscle
31	chr3:52109200-52114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:52109400-52111200	Genic enhancers	Fetal Stomach	stomach
33	chr3:52109400-52111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:52109400-52112000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:52109400-52115000	Weak transcription	Gastric	stomach
36	chr3:52109600-52113800	Weak transcription	HepG2	liver
37	chr3:52109600-52123800	Weak transcription	NHEK	skin
38	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:52109800-52111600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:52109800-52112400	Enhancers	Brain Hippocampus Middle	brain
41	chr3:52110000-52111400	Weak transcription	Fetal Thymus	thymus
42	chr3:52110000-52112000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:52110000-52112000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:52110000-52112400	Enhancers	Brain Cingulate Gyrus	brain
45	chr3:52110000-52112800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:52110000-52114800	Weak transcription	Fetal Intestine Small	intestine
47	chr3:52110000-52120000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:52110000-52121600	Weak transcription	NHLF	lung
49	chr3:52110000-52122000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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