Variant report

Variant	rs73935050
Chromosome Location	chr19:52733048-52733049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52692286..52695844-chr19:52730833..52733280,4	MCF-7	breast:
2	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10409071	1.00[ASN][1000 genomes]
rs10416397	1.00[ASN][1000 genomes]
rs11537695	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382052	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275796	1.00[ASN][1000 genomes]
rs41275802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071533	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58576324	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61285115	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717322	1.00[ASN][1000 genomes]
rs73934406	1.00[ASN][1000 genomes]
rs73934407	1.00[ASN][1000 genomes]
rs73935029	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935031	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935032	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935039	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935040	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935041	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52695400-52733200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr19:52697600-52733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr19:52703000-52734600	Strong transcription	Fetal Stomach	stomach
4	chr19:52703200-52733200	Strong transcription	Duodenum Mucosa	Duodenum
5	chr19:52703200-52734000	Strong transcription	Lung	lung
6	chr19:52703600-52733200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:52703800-52733200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:52704000-52733200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:52704400-52733200	Strong transcription	Osteobl	bone
10	chr19:52705000-52735200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr19:52709000-52733200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:52713000-52733400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:52718000-52734200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:52719000-52735400	ZNF genes & repeats	A549	lung
15	chr19:52722200-52733200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr19:52723600-52735200	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:52723800-52733400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:52727200-52733400	Strong transcription	Fetal Intestine Small	intestine
19	chr19:52727600-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:52730200-52734400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:52730200-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:52730400-52734000	Weak transcription	Small Intestine	intestine
23	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr19:52731000-52736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:52731000-52736800	Weak transcription	Stomach Mucosa	stomach
26	chr19:52731200-52734400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:52731600-52733200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:52731600-52733200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:52731600-52733200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:52731600-52733200	Weak transcription	Fetal Kidney	kidney
31	chr19:52731600-52734600	Weak transcription	Aorta	Aorta
32	chr19:52731600-52736400	Weak transcription	Fetal Heart	heart
33	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
34	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:52731800-52733400	Weak transcription	K562	blood
36	chr19:52731800-52735400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:52731800-52736600	Weak transcription	HUVEC	blood vessel
38	chr19:52732000-52733600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr19:52732000-52734400	Weak transcription	NHDF-Ad	bronchial
40	chr19:52732000-52736000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:52732000-52736000	Weak transcription	Psoas Muscle	Psoas
42	chr19:52732000-52736600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:52732200-52733200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:52732200-52733800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:52732200-52733800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:52732200-52733800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:52732200-52733800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:52732200-52733800	Weak transcription	NHEK	skin

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