Variant report

Variant	rs2064760
Chromosome Location	chr10:52269914-52269915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52268790..52270873-chr10:52275061..52278786,3	MCF-7	breast:
2	chr10:52261680..52263393-chr10:52269137..52270888,2	MCF-7	breast:
3	chr10:52269188..52271460-chr10:52277484..52280153,2	MCF-7	breast:
4	chr10:52269833..52272327-chr17:57922968..57924991,2	MCF-7	breast:
5	chr10:52264079..52265677-chr10:52268194..52270152,2	K562	blood:

Variant related genes	Relation type
ENSG00000201524	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10082515	0.91[JPT][hapmap]
rs1028534	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10826014	0.91[JPT][hapmap]
rs10826126	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11005720	0.90[JPT][hapmap]
rs1203374	0.80[EUR][1000 genomes]
rs1203379	0.89[EUR][1000 genomes]
rs1203380	0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1203383	0.93[TSI][hapmap]
rs1203384	0.80[EUR][1000 genomes]
rs1203391	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs1203402	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs1203412	0.80[EUR][1000 genomes]
rs1203426	0.80[EUR][1000 genomes]
rs1203427	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs1209146	0.80[EUR][1000 genomes]
rs1211373	0.80[EUR][1000 genomes]
rs1212555	0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap]
rs12569801	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12569909	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12571095	0.94[ASN][1000 genomes]
rs12573520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13376734	0.83[TSI][hapmap]
rs16937491	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16937722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16937771	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16937775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16937786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17179881	0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1880071	0.94[ASN][1000 genomes]
rs2024871	0.89[EUR][1000 genomes]
rs2208035	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs2842110	0.89[TSI][hapmap]
rs2983346	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983348	0.85[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2983349	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983372	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs3001853	0.86[TSI][hapmap]
rs3011712	0.89[EUR][1000 genomes]
rs3011715	0.91[EUR][1000 genomes]
rs3011768	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs3011795	0.89[EUR][1000 genomes]
rs3739990	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs41427847	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs57015168	0.95[ASN][1000 genomes]
rs57748270	0.93[ASN][1000 genomes]
rs57999700	0.98[ASN][1000 genomes]
rs58383805	0.87[ASN][1000 genomes]
rs58642196	0.88[ASN][1000 genomes]
rs59510112	0.88[ASN][1000 genomes]
rs59512026	0.95[ASN][1000 genomes]
rs66546375	0.90[ASN][1000 genomes]
rs67761241	0.95[ASN][1000 genomes]
rs7075289	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7077555	0.86[TSI][hapmap]
rs7897345	0.86[TSI][hapmap]
rs7923756	0.89[TSI][hapmap]
rs910818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910819	0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9416590	0.89[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2064760	DAPK1	trans	lymphoblastoid	seeQTL
rs2064760	CSTF2T	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:52261800-52271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:52262000-52270800	Weak transcription	HSMMtube	muscle
5	chr10:52262200-52271200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:52262400-52270600	Weak transcription	Primary T cells from cord blood	blood
8	chr10:52262400-52271800	Weak transcription	Fetal Stomach	stomach
9	chr10:52262400-52272600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:52262600-52271200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:52262800-52273000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:52263800-52271400	Weak transcription	Placenta	Placenta
13	chr10:52263800-52271800	Weak transcription	Esophagus	oesophagus
14	chr10:52264200-52270800	Weak transcription	K562	blood
15	chr10:52264600-52271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:52264800-52271000	Weak transcription	NHEK	skin
17	chr10:52265000-52271200	Enhancers	Brain Cingulate Gyrus	brain
18	chr10:52265000-52272400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr10:52265400-52270000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:52265400-52270400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr10:52265400-52273200	Enhancers	Brain Angular Gyrus	brain
22	chr10:52266200-52272800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr10:52266400-52272800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:52266400-52272800	Enhancers	HepG2	liver
25	chr10:52266800-52271200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:52267000-52272400	Weak transcription	Thymus	Thymus
28	chr10:52267000-52273400	Enhancers	Brain Substantia Nigra	brain
29	chr10:52267000-52282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr10:52267400-52271000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr10:52267400-52271800	Weak transcription	Lung	lung
32	chr10:52267400-52273600	Enhancers	Brain Hippocampus Middle	brain
33	chr10:52267600-52270800	Weak transcription	Fetal Heart	heart
34	chr10:52267600-52271000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:52267600-52272400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr10:52267600-52273000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:52267600-52273000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr10:52267600-52277800	Enhancers	Brain Anterior Caudate	brain
39	chr10:52267800-52270000	Enhancers	Fetal Intestine Large	intestine
40	chr10:52267800-52271600	Weak transcription	Ovary	ovary
41	chr10:52268000-52270000	Enhancers	Liver	Liver
42	chr10:52268000-52273200	Enhancers	Stomach Mucosa	stomach
43	chr10:52268200-52270200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr10:52268200-52270800	Weak transcription	Right Ventricle	heart
45	chr10:52268200-52271000	Weak transcription	Left Ventricle	heart
46	chr10:52268200-52271400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:52268200-52271600	Enhancers	Fetal Lung	lung
48	chr10:52268200-52282400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr10:52268200-52282600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:52268400-52270800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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