Variant report

Variant	rs11717931
Chromosome Location	chr3:53924379-53924380
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
2	chr3:53909521..53911477-chr3:53924349..53927028,2	MCF-7	breast:
3	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
4	chr3:53921644..53923214-chr3:53923445..53925751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222888	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11714234	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11718358	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276842	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715733	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733082	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774626	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4687593	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4687596	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687754	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4687759	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55835925	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56708826	0.88[AFR][1000 genomes]
rs57777269	0.88[AFR][1000 genomes]
rs726028	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744381	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628619	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636572	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7646455	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53916200-53924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:53916200-53924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53916600-53924400	Weak transcription	Fetal Kidney	kidney
4	chr3:53916600-53924800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:53916600-53924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:53916600-53924800	Weak transcription	Aorta	Aorta
7	chr3:53916800-53924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:53916800-53924600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:53916800-53924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:53918000-53924800	Weak transcription	Esophagus	oesophagus
11	chr3:53919600-53925200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:53920000-53924800	Weak transcription	Lung	lung
13	chr3:53920200-53924400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:53920200-53924400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:53920400-53924800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:53920400-53924800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:53920600-53924400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:53920800-53924800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:53921400-53924400	Weak transcription	Fetal Stomach	stomach
20	chr3:53921400-53924600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:53921800-53924800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:53921800-53924800	Weak transcription	Pancreas	Pancrea
23	chr3:53922000-53924600	Enhancers	Fetal Heart	heart
24	chr3:53922200-53924600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:53922200-53924800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:53922200-53924800	Weak transcription	Placenta	Placenta
27	chr3:53922400-53924400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:53922400-53924400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:53922400-53924600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:53922400-53924600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:53922400-53925000	Enhancers	Small Intestine	intestine
32	chr3:53922600-53924400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:53922600-53924600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:53922600-53924800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:53922800-53924400	Weak transcription	Primary B cells from cord blood	blood
36	chr3:53922800-53924400	Weak transcription	K562	blood
37	chr3:53922800-53924800	Enhancers	Primary T cells from cord blood	blood
38	chr3:53923000-53924800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:53923200-53924400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:53923200-53924600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:53923400-53924400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:53923400-53924600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:53923400-53924600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:53923400-53924600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr3:53923400-53924800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:53923400-53924800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:53923400-53925000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr3:53923400-53926400	Active TSS	Right Ventricle	heart
49	chr3:53923600-53924400	Enhancers	HepG2	liver
50	chr3:53923600-53924600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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