Variant report

Variant	rs2972456
Chromosome Location	chr19:38138339-38138340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38085270..38087248-chr19:38138065..38140265,2	MCF-7	breast:
2	chr19:38136998..38138524-chr19:38142889..38145003,2	MCF-7	breast:
3	chr19:38137873..38139917-chr19:38145881..38147430,2	K562	blood:

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction
ENSG00000120784	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1038084	0.89[CEU][hapmap]
rs1038085	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407657	0.85[CEU][hapmap]
rs10417204	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10424612	0.89[CEU][hapmap]
rs10425671	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665877	0.90[EUR][1000 genomes]
rs11667454	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667457	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11668558	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11670655	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883392	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1236810	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12972712	0.91[EUR][1000 genomes]
rs12981237	0.90[EUR][1000 genomes]
rs12982288	0.91[EUR][1000 genomes]
rs12983298	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17306508	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17306795	1.00[CHB][hapmap]
rs1871197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045909	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126978	0.84[CEU][hapmap]
rs2160640	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199644	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291000	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385124	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385125	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs241937	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241940	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241941	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs241942	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241947	0.86[EUR][1000 genomes]
rs241948	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs241951	1.00[CHB][hapmap]
rs241953	0.85[EUR][1000 genomes]
rs2617789	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2909106	0.84[EUR][1000 genomes]
rs2927741	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927744	0.85[CEU][hapmap]
rs2972453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972454	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112435	0.91[EUR][1000 genomes]
rs34351186	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607899	0.92[EUR][1000 genomes]
rs34782935	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34949193	0.85[EUR][1000 genomes]
rs35015599	0.91[EUR][1000 genomes]
rs35214625	0.91[EUR][1000 genomes]
rs35273320	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35415221	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36020184	0.89[EUR][1000 genomes]
rs36092052	0.89[EUR][1000 genomes]
rs3752365	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4273159	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4802066	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802069	0.85[CEU][hapmap]
rs4803216	0.89[CEU][hapmap]
rs4803228	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57308437	0.91[EUR][1000 genomes]
rs62108304	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108339	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62108355	0.89[EUR][1000 genomes]
rs6508729	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6508738	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251097	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7253174	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254170	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254828	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7255283	0.85[CEU][hapmap]
rs8111055	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8113076	0.85[CEU][hapmap]
rs856302	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38121800-38139200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:38121800-38140600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:38123400-38138800	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:38123600-38140000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:38123600-38140800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:38123600-38141400	ZNF genes & repeats	Liver	Liver
7	chr19:38124600-38140800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:38124600-38142000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:38124800-38143200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:38124800-38144400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:38125600-38143200	ZNF genes & repeats	A549	lung
12	chr19:38125800-38139600	ZNF genes & repeats	Colon Smooth Muscle	Colon
13	chr19:38125800-38140800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr19:38126000-38141400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:38126200-38143200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:38126400-38139400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
17	chr19:38127200-38144600	Weak transcription	Hela-S3	cervix
18	chr19:38129200-38138400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:38129200-38139600	Strong transcription	HSMM	muscle
20	chr19:38129600-38139000	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr19:38130000-38141600	Strong transcription	Osteobl	bone
22	chr19:38130400-38138400	Strong transcription	Brain Germinal Matrix	brain
23	chr19:38130400-38142200	ZNF genes & repeats	GM12878-XiMat	blood
24	chr19:38130600-38139800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:38131000-38139200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr19:38131000-38141000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:38131600-38139200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:38131600-38141200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:38131800-38138800	Strong transcription	Brain Anterior Caudate	brain
30	chr19:38131800-38139000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:38131800-38140600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:38132000-38138600	Strong transcription	Fetal Brain Male	brain
33	chr19:38132000-38138800	Strong transcription	HSMMtube	muscle
34	chr19:38132000-38139000	ZNF genes & repeats	Ovary	ovary
35	chr19:38132000-38139800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr19:38132200-38139000	Strong transcription	Placenta	Placenta
37	chr19:38132200-38139200	Strong transcription	Brain Angular Gyrus	brain
38	chr19:38132200-38139400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr19:38132400-38138800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:38132400-38139000	Strong transcription	Fetal Thymus	thymus
41	chr19:38132400-38139200	Strong transcription	Brain Substantia Nigra	brain
42	chr19:38132400-38139400	Strong transcription	Brain Hippocampus Middle	brain
43	chr19:38132600-38138800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:38132600-38139200	Strong transcription	HepG2	liver
45	chr19:38133000-38138800	Strong transcription	Fetal Kidney	kidney
46	chr19:38133000-38139000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:38133000-38139200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr19:38133000-38139200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr19:38133000-38139200	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:38133000-38139200	Strong transcription	Skeletal Muscle Male	skeletal muscle

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