Variant report

Variant	rs9860982
Chromosome Location	chr3:52096432-52096433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52094254..52096500-chr3:52125955..52128876,2	MCF-7	breast:
2	chr3:52089468..52092661-chr3:52093229..52096649,5	K562	blood:
3	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf74-1	chr3:52096110-52099128	NONHSAT089896

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs123681	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12386365	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13314125	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13319566	0.89[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164638	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs164639	0.89[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17051957	0.90[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17051977	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171294	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs183029	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304505	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452586	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28659792	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs352146	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs352147	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352148	0.89[CEU][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352149	0.89[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352150	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352151	0.89[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352153	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755797	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs55664415	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55834589	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56281986	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56322622	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57335685	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57466127	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59890038	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6781635	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72964042	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72964044	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638246	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs808787	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs876782	0.89[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs893056	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs9809254	0.89[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9809977	0.81[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9811707	0.81[ASW][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9815010	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9816434	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9817653	0.81[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9830293	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9841469	0.89[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843299	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843852	0.89[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9846049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9847073	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9847092	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9857878	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs9865330	0.94[GIH][hapmap];0.88[TSI][hapmap]
rs9868101	0.89[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882775	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh 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
3	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
4	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
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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
6	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
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv590293	chr3:52089889-52097060	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv590299	chr3:52090344-52096432	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv590300	chr3:52090597-52096432	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091800-52101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
3	chr3:52092000-52096800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52092000-52097600	Enhancers	GM12878-XiMat	blood
5	chr3:52092000-52099200	Weak transcription	Right Atrium	heart
6	chr3:52092000-52102200	Enhancers	HMEC	breast
7	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:52092200-52096600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:52092200-52096600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:52092200-52096600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:52092200-52096600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:52092200-52096600	Weak transcription	Right Ventricle	heart
13	chr3:52092200-52096800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:52092200-52096800	Weak transcription	Fetal Brain Male	brain
15	chr3:52092200-52099200	Weak transcription	Gastric	stomach
16	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
19	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:52092400-52096600	Weak transcription	Colonic Mucosa	Colon
23	chr3:52092400-52096600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:52094000-52102000	Enhancers	NHEK	skin
26	chr3:52094200-52096600	Weak transcription	Spleen	Spleen
27	chr3:52094200-52098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:52094600-52096600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:52094600-52097200	Enhancers	Stomach Mucosa	stomach
30	chr3:52094800-52097000	Enhancers	Lung	lung
31	chr3:52094800-52097400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:52094800-52097800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr3:52095000-52097400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:52095200-52096600	Enhancers	Adipose Nuclei	Adipose
35	chr3:52095200-52097800	Enhancers	Placenta	Placenta
36	chr3:52095400-52097200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:52095600-52097800	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:52095800-52096600	Enhancers	Primary B cells from cord blood	blood
39	chr3:52095800-52096800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:52095800-52097000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:52095800-52097000	Enhancers	Left Ventricle	heart
42	chr3:52095800-52097200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:52095800-52097800	Enhancers	Fetal Muscle Leg	muscle
44	chr3:52096000-52099200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52096200-52096600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:52096200-52096800	Enhancers	Colon Smooth Muscle	Colon
48	chr3:52096200-52097000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr3:52096200-52097400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:52096200-52097600	Enhancers	Brain Hippocampus Middle	brain

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