Variant report

Variant	rs12975011
Chromosome Location	chr19:51851069-51851070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51848237..51856350-chr19:51866106..51872931,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269403	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000160318	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12976097	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977906	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979526	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981254	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411326	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59890391	0.94[EUR][1000 genomes]
rs8102334	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8102664	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8107232	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107235	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107468	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv912294	chr19:51844978-51878841	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51843000-51852200	Weak transcription	Fetal Heart	heart
2	chr19:51843000-51857600	Weak transcription	Fetal Kidney	kidney
3	chr19:51843200-51857400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:51843600-51854000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:51843800-51854400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:51843800-51857600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:51844000-51851800	Weak transcription	HSMM	muscle
8	chr19:51844000-51852000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:51844000-51857400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:51844000-51865800	Weak transcription	Small Intestine	intestine
11	chr19:51844000-51866400	Weak transcription	Right Atrium	heart
12	chr19:51844200-51853400	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:51844200-51854200	Weak transcription	Psoas Muscle	Psoas
14	chr19:51844200-51857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:51844200-51857600	Weak transcription	NH-A	brain
16	chr19:51845800-51856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:51846000-51857600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:51846200-51852800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:51846200-51856400	Weak transcription	Fetal Brain Male	brain
20	chr19:51846200-51857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:51846200-51857600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:51846400-51854200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:51846400-51857200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:51846400-51857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:51846400-51857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:51846400-51857400	Weak transcription	Stomach Mucosa	stomach
27	chr19:51846600-51855600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:51846600-51857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:51846600-51857600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:51847200-51851200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:51847200-51851200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:51847200-51856600	Strong transcription	Fetal Stomach	stomach
33	chr19:51847200-51868600	Weak transcription	Fetal Lung	lung
34	chr19:51847400-51851200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:51847400-51851200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:51847400-51851200	Strong transcription	Thymus	Thymus
37	chr19:51847400-51851200	Strong transcription	Dnd41	blood
38	chr19:51847400-51851400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:51847400-51851400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr19:51847400-51851800	Strong transcription	Left Ventricle	heart
41	chr19:51847400-51856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:51847400-51856600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:51847400-51858200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr19:51847600-51856600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:51847800-51851200	Strong transcription	Spleen	Spleen
46	chr19:51847800-51851400	Strong transcription	Fetal Intestine Large	intestine
47	chr19:51847800-51856800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:51848000-51851200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:51848000-51851200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr19:51848000-51851200	Strong transcription	Lung	lung

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