Variant report

Variant	rs12972660
Chromosome Location	chr19:36617502-36617503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36583233..36586201-chr19:36617082..36618818,2	K562	blood:
2	chr19:36615077..36620423-chr19:36622100..36624907,6	K562	blood:
3	chr19:36617317..36620455-chr19:36659858..36661867,3	MCF-7	breast:
4	chr19:36610352..36613134-chr19:36616460..36619107,3	K562	blood:
5	chr19:36617223..36621168-chr19:36621174..36623571,4	MCF-7	breast:
6	chr19:36616979..36620071-chr19:36629993..36632800,4	K562	blood:
7	chr19:36617250..36625256-chr19:36625801..36633837,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105254	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10407011	0.87[ASN][1000 genomes]
rs10426582	0.85[AMR][1000 genomes]
rs12977802	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12979093	0.85[AMR][1000 genomes]
rs2072606	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2075474	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239510	0.87[ASN][1000 genomes]
rs34906485	0.80[AMR][1000 genomes]
rs3810445	0.81[EUR][1000 genomes]
rs4805154	0.81[AMR][1000 genomes]
rs4805155	0.84[AMR][1000 genomes]
rs4806252	0.84[AMR][1000 genomes]
rs4806253	0.85[AMR][1000 genomes]
rs4806279	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806280	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56034793	0.85[AMR][1000 genomes]
rs62109743	0.85[AMR][1000 genomes]
rs7245762	0.84[AMR][1000 genomes]
rs7250448	0.85[AMR][1000 genomes]
rs7257383	0.85[AMR][1000 genomes]
rs8100250	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh 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	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36607200-36618600	Weak transcription	Psoas Muscle	Psoas
2	chr19:36607400-36618400	Weak transcription	Stomach Mucosa	stomach
3	chr19:36607400-36618600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:36607400-36618800	Weak transcription	Small Intestine	intestine
5	chr19:36607600-36618400	Weak transcription	K562	blood
6	chr19:36608000-36617800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr19:36608000-36618000	Strong transcription	Fetal Stomach	stomach
8	chr19:36608200-36618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:36611600-36618000	Strong transcription	Fetal Intestine Small	intestine
10	chr19:36612600-36618000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:36613600-36618400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:36614000-36618400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:36614200-36618800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:36615200-36618200	Weak transcription	Pancreas	Pancrea
15	chr19:36615200-36618400	Weak transcription	Primary B cells from cord blood	blood
16	chr19:36615200-36618400	Weak transcription	HUVEC	blood vessel
17	chr19:36615200-36618600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:36615400-36618600	Weak transcription	Fetal Brain Male	brain
19	chr19:36616600-36618200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:36616600-36618200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:36616600-36618600	Weak transcription	HSMMtube	muscle
22	chr19:36616600-36619000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:36616800-36618200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:36616800-36618400	Weak transcription	Brain Substantia Nigra	brain
25	chr19:36616800-36618400	Weak transcription	Colonic Mucosa	Colon
26	chr19:36616800-36618400	Weak transcription	Fetal Kidney	kidney
27	chr19:36616800-36618400	Weak transcription	Hela-S3	cervix
28	chr19:36616800-36618600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:36616800-36618600	Weak transcription	NH-A	brain
30	chr19:36616800-36619000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36617000-36618200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:36617000-36618200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:36617000-36618200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr19:36617000-36618200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:36617000-36618200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:36617000-36618200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:36617000-36618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:36617000-36618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:36617000-36618200	Weak transcription	Fetal Muscle Leg	muscle
40	chr19:36617000-36618200	Weak transcription	Fetal Thymus	thymus
41	chr19:36617000-36618200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:36617000-36618200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:36617000-36618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:36617000-36618200	Weak transcription	GM12878-XiMat	blood
45	chr19:36617000-36618400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:36617000-36618400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:36617000-36618400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:36617000-36618400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:36617000-36618400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:36617000-36618400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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