Variant report

Variant	rs57999700
Chromosome Location	chr10:52274971-52274972
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52272048..52276086-chr10:52381938..52384651,3	MCF-7	breast:
2	chr10:52271127..52273442-chr10:52273762..52275494,2	MCF-7	breast:
3	chr10:52271610..52273554-chr10:52274092..52276247,2	MCF-7	breast:
4	chr10:52260554..52263861-chr10:52272806..52275340,3	K562	blood:
5	chr10:52272629..52275165-chr10:52281578..52283752,2	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028534	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12569801	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12569909	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12571095	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12573520	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16937491	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16937722	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937771	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16937775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16937786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1880071	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064760	0.98[ASN][1000 genomes]
rs2983346	0.93[ASN][1000 genomes]
rs2983349	0.93[ASN][1000 genomes]
rs3739990	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41427847	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57015168	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57748270	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58383805	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58642196	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59510112	0.87[ASN][1000 genomes]
rs59512026	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66546375	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67761241	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910818	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:52267000-52282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr10:52267600-52277800	Enhancers	Brain Anterior Caudate	brain
5	chr10:52268200-52282400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:52268200-52282600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr10:52268400-52282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:52268800-52278800	Weak transcription	Primary B cells from cord blood	blood
9	chr10:52270000-52282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr10:52270000-52282800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:52270200-52282600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:52271200-52283000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:52271600-52276800	Weak transcription	Fetal Lung	lung
14	chr10:52271600-52277400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
16	chr10:52271800-52280800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:52272200-52281000	Weak transcription	Fetal Intestine Large	intestine
18	chr10:52272400-52275600	Weak transcription	Fetal Heart	heart
19	chr10:52272400-52280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr10:52272400-52280400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr10:52272400-52284600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
23	chr10:52272800-52275000	Weak transcription	Psoas Muscle	Psoas
24	chr10:52272800-52275200	Weak transcription	Esophagus	oesophagus
25	chr10:52272800-52275800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:52272800-52276000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:52272800-52279000	Weak transcription	Fetal Intestine Small	intestine
28	chr10:52272800-52281200	Weak transcription	Ovary	ovary
29	chr10:52272800-52281400	Weak transcription	Placenta	Placenta
30	chr10:52272800-52281600	Weak transcription	HepG2	liver
31	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
32	chr10:52273000-52275000	Enhancers	HMEC	breast
33	chr10:52273000-52275200	Enhancers	NHEK	skin
34	chr10:52273000-52275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr10:52273200-52275200	Weak transcription	Gastric	stomach
36	chr10:52273200-52278200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:52273200-52278600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr10:52273200-52279000	Weak transcription	Lung	lung
39	chr10:52273200-52281000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr10:52273200-52281600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:52273200-52282600	Weak transcription	Right Ventricle	heart
42	chr10:52273200-52285800	Weak transcription	K562	blood
43	chr10:52273200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:52273200-52287400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:52273400-52275000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr10:52273400-52275400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr10:52273400-52278400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:52273400-52279000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:52273400-52279200	Weak transcription	Primary T cells fromperipheralblood	blood

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