Variant report

Variant	rs3011770
Chromosome Location	chr10:52271385-52271386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52269188..52271460-chr10:52277484..52280153,2	MCF-7	breast:
2	chr10:52264059..52268097-chr10:52270623..52273217,5	K562	blood:
3	chr10:52269936..52272256-chr10:52382493..52385087,2	K562	blood:
4	chr10:52269833..52272327-chr17:57922968..57924991,2	MCF-7	breast:
5	chr10:52226422..52229059-chr10:52270774..52272977,2	MCF-7	breast:
6	chr10:52228792..52231696-chr10:52270677..52273544,2	MCF-7	breast:
7	chr10:52266589..52268433-chr10:52270760..52273217,2	K562	blood:
8	chr10:52271127..52273442-chr10:52273762..52275494,2	MCF-7	breast:
9	chr10:52270406..52272134-chr10:52383190..52385658,2	MCF-7	breast:
10	chr10:52270150..52272703-chr10:52318825..52321110,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10159614	0.82[ASW][hapmap];0.90[LWK][hapmap]
rs11005901	0.82[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs1203382	0.90[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1203386	0.90[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs1203394	0.90[CEU][hapmap]
rs1203395	0.80[AMR][1000 genomes]
rs1203401	0.92[AMR][1000 genomes]
rs1203403	0.94[AMR][1000 genomes]
rs1203405	0.82[AMR][1000 genomes]
rs1203407	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs1203409	0.90[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs1203410	0.90[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs1203411	0.92[AMR][1000 genomes]
rs1203418	0.84[MEX][hapmap]
rs12265364	1.00[YRI][hapmap]
rs1740761	0.90[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2221	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs2574985	0.84[MEX][hapmap]
rs2983347	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2983350	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs2983354	0.93[CEU][hapmap];0.85[AMR][1000 genomes]
rs2983357	0.85[CEU][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs2983359	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs2983361	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs2983368	0.90[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2983369	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2983370	0.81[AMR][1000 genomes]
rs2983371	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3011771	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3011773	0.90[CEU][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3011779	0.85[AMR][1000 genomes]
rs3011780	0.85[AMR][1000 genomes]
rs3011782	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs3011783	0.85[AMR][1000 genomes]
rs3011786	0.85[AMR][1000 genomes]
rs3011787	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3011788	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs3011789	0.85[AMR][1000 genomes]
rs3011790	0.85[CEU][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs3011791	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs3011792	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs3011793	0.88[AMR][1000 genomes]
rs3011794	0.85[CEU][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs3011797	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs3011801	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs920136	0.84[MEX][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3011770	MSMB	cis	parietal	SCAN
rs3011770	PARG	cis	parietal	SCAN
rs3011770	PRKG1	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr10:52261800-52271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:52262400-52271800	Weak transcription	Fetal Stomach	stomach
5	chr10:52262400-52272600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:52262800-52273000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:52263800-52271400	Weak transcription	Placenta	Placenta
8	chr10:52263800-52271800	Weak transcription	Esophagus	oesophagus
9	chr10:52264600-52271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:52265000-52272400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr10:52265400-52273200	Enhancers	Brain Angular Gyrus	brain
12	chr10:52266200-52272800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr10:52266400-52272800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:52266400-52272800	Enhancers	HepG2	liver
15	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr10:52267000-52272400	Weak transcription	Thymus	Thymus
17	chr10:52267000-52273400	Enhancers	Brain Substantia Nigra	brain
18	chr10:52267000-52282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:52267400-52271800	Weak transcription	Lung	lung
20	chr10:52267400-52273600	Enhancers	Brain Hippocampus Middle	brain
21	chr10:52267600-52272400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr10:52267600-52273000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:52267600-52273000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr10:52267600-52277800	Enhancers	Brain Anterior Caudate	brain
25	chr10:52267800-52271600	Weak transcription	Ovary	ovary
26	chr10:52268000-52273200	Enhancers	Stomach Mucosa	stomach
27	chr10:52268200-52271400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:52268200-52271600	Enhancers	Fetal Lung	lung
29	chr10:52268200-52282400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr10:52268200-52282600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:52268400-52282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr10:52268800-52271400	Weak transcription	Gastric	stomach
33	chr10:52268800-52271600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:52268800-52271800	Weak transcription	Fetal Muscle Leg	muscle
35	chr10:52268800-52272200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr10:52268800-52278800	Weak transcription	Primary B cells from cord blood	blood
37	chr10:52269200-52273000	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr10:52269400-52272200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:52270000-52271800	Weak transcription	Liver	Liver
40	chr10:52270000-52271800	Weak transcription	Fetal Intestine Large	intestine
41	chr10:52270000-52282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:52270000-52282800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr10:52270200-52282600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr10:52270400-52271600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:52270400-52273000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr10:52270600-52271400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:52270600-52272200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:52270600-52272200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr10:52270600-52272800	Enhancers	Primary T cells from cord blood	blood
50	chr10:52270800-52271600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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