Variant report

Variant	rs12980942
Chromosome Location	chr19:41832231-41832232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41767658..41770792-chr19:41831725..41834238,3	K562	blood:
2	chr19:41826823..41830968-chr19:41831922..41834042,4	K562	blood:
3	chr19:41831560..41835425-chr19:41857306..41860915,5	MCF-7	breast:
4	chr19:41831768..41836591-chr19:41855042..41861850,7	MCF-7	breast:
5	chr19:41828482..41836150-chr19:41836490..41842395,12	K562	blood:
6	chr19:41811198..41813629-chr19:41830281..41833026,2	K562	blood:
7	chr19:41816132..41816899-chr19:41832020..41832852,2	K562	blood:
8	chr19:41830987..41833840-chr19:41863132..41865918,2	MCF-7	breast:
9	chr19:41831305..41834013-chr19:41846583..41848219,2	MCF-7	breast:
10	chr19:41710873..41712522-chr19:41830997..41833166,2	K562	blood:
11	chr19:41832231..41833796-chr19:41933129..41935701,2	MCF-7	breast:
12	chr19:41771700..41774253-chr19:41830913..41833263,2	K562	blood:
13	chr19:41831346..41834829-chr19:41839847..41842634,3	MCF-7	breast:
14	chr19:41832138..41834611-chr19:41867013..41869062,2	K562	blood:
15	chr19:41831307..41833980-chr19:41944294..41947067,2	MCF-7	breast:
16	chr19:41827333..41835079-chr19:41855373..41860241,10	K562	blood:
17	chr19:41769289..41771419-chr19:41832191..41834846,3	MCF-7	breast:
18	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:
19	chr19:41831464..41833596-chr19:41945378..41947616,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105323	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000255730	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10421990	0.85[CEU][hapmap]
rs1056854	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs11466345	0.81[JPT][hapmap]
rs11466347	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11466359	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11879429	0.87[ASN][1000 genomes]
rs11879435	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11879562	0.85[CEU][hapmap]
rs11880564	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11880729	0.87[ASN][1000 genomes]
rs11881940	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11881953	0.99[ASN][1000 genomes]
rs12327659	0.85[CEU][hapmap]
rs12972266	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12972949	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12974420	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12976536	0.99[ASN][1000 genomes]
rs12977563	0.87[ASN][1000 genomes]
rs12980267	0.92[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12980298	0.98[EUR][1000 genomes]
rs12980480	0.85[CEU][hapmap]
rs12981053	0.80[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983047	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12983339	0.89[ASN][1000 genomes]
rs12984160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985339	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16958994	0.82[EUR][1000 genomes]
rs16958996	0.82[EUR][1000 genomes]
rs16958999	0.82[EUR][1000 genomes]
rs1865051	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1865052	0.82[EUR][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1946612	0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1946613	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2053086	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2241718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241719	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304230	0.85[CEU][hapmap]
rs2304231	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2304232	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34075897	0.86[EUR][1000 genomes]
rs34322801	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34772093	0.81[ASN][1000 genomes]
rs34945449	0.82[EUR][1000 genomes]
rs35501756	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35546772	0.82[ASN][1000 genomes]
rs35812313	0.92[ASN][1000 genomes]
rs3745295	0.85[CEU][hapmap]
rs3752705	0.85[CEU][hapmap]
rs3760659	0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3760660	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3816052	0.85[CEU][hapmap]
rs3826714	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4456618	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4591267	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs61459202	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67511749	0.82[EUR][1000 genomes]
rs67744888	0.92[ASN][1000 genomes]
rs6957	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7248164	0.85[CEU][hapmap]
rs7250883	0.92[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7254679	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7257310	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7257742	0.86[EUR][1000 genomes]
rs7258749	0.85[CEU][hapmap]
rs8103839	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8105161	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs8105901	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8109167	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911769	chr19:41813676-41845801	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41818600-41854800	Strong transcription	Dnd41	blood
2	chr19:41824400-41834000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:41827000-41832800	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr19:41827400-41833000	Enhancers	Primary hematopoietic stem cells	blood
5	chr19:41827400-41833000	Genic enhancers	Fetal Thymus	thymus
6	chr19:41828600-41834000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr19:41828800-41832400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:41828800-41834000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:41828800-41834400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:41829200-41835400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr19:41829600-41833000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr19:41830000-41832600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:41830000-41833000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:41830000-41833400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:41830200-41832400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:41830200-41833200	Enhancers	HMEC	breast
17	chr19:41830400-41832400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr19:41830400-41832400	Weak transcription	NHEK	skin
19	chr19:41830400-41834000	Enhancers	Fetal Lung	lung
20	chr19:41830600-41832400	Flanking Active TSS	NH-A	brain
21	chr19:41830600-41832600	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr19:41830600-41833000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:41830800-41832600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:41830800-41834600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:41830800-41835000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:41831200-41832400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:41831200-41832400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr19:41831200-41832400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:41831200-41832400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:41831200-41832400	Flanking Active TSS	Pancreas	Pancrea
31	chr19:41831200-41833000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr19:41831200-41833000	Weak transcription	Thymus	Thymus
33	chr19:41831600-41832400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:41831600-41832400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr19:41831600-41832400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:41831600-41832400	Flanking Active TSS	HUVEC	blood vessel
37	chr19:41831600-41832400	Flanking Active TSS	Osteobl	bone
38	chr19:41831600-41832600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
39	chr19:41831600-41832600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:41831600-41832800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr19:41831600-41834000	Genic enhancers	Primary T cells from cord blood	blood
42	chr19:41831600-41835200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr19:41831600-41835400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr19:41831800-41832400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:41831800-41832400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
46	chr19:41831800-41832400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr19:41831800-41832400	Flanking Active TSS	HepG2	liver
48	chr19:41831800-41832600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr19:41831800-41832600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:41831800-41832600	Flanking Active TSS	Rectal Smooth Muscle	rectum

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