Variant report

Variant	rs10882993
Chromosome Location	chr10:99504630-99504631
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99503209..99504783-chr10:99507206..99509576,2	MCF-7	breast:
2	chr10:99496561..99499053-chr10:99501574..99505641,4	MCF-7	breast:
3	chr10:99495422..99498377-chr10:99503032..99505920,4	MCF-7	breast:
4	chr10:99503362..99505706-chr10:99509652..99511798,2	K562	blood:
5	chr10:99494917..99500697-chr10:99501380..99508176,12	K562	blood:
6	chr10:99503150..99505719-chr10:99507042..99510106,3	MCF-7	breast:
7	chr10:99500286..99501793-chr10:99503721..99505250,2	MCF-7	breast:
8	chr10:99503270..99505522-chr10:99510241..99512787,2	MCF-7	breast:
9	chr10:99499187..99502135-chr10:99502777..99505222,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10748708	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10748709	0.81[ASN][1000 genomes]
rs10786367	0.95[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap]
rs10786370	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10786371	0.95[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs10786372	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs10882994	0.85[EUR][1000 genomes]
rs10882995	0.85[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs10882998	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11189353	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs11189355	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs11189357	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs11189360	0.80[CEU][hapmap]
rs11189361	0.81[ASN][1000 genomes]
rs11189362	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11591898	0.83[EUR][1000 genomes]
rs1538723	0.83[EUR][1000 genomes]
rs1556971	0.83[ASN][1000 genomes]
rs1981237	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs1981238	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs2027376	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2039826	0.80[CEU][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs3750612	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3750614	1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs3750615	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs3814558	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs3814559	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3814560	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs4244329	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs4917784	0.83[JPT][hapmap]
rs4919139	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs7077725	0.84[ASN][1000 genomes]
rs7080894	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7080953	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7081652	0.83[ASN][1000 genomes]
rs7099540	0.80[CEU][hapmap]
rs7907679	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7910589	0.81[ASN][1000 genomes]
rs7916164	0.88[ASN][1000 genomes]
rs7916454	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs7916593	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7922907	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883324	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs946777	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs946778	1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10882993	COX15	cis	cerebellum	SCAN
rs10882993	C10orf12	cis	cerebellum	SCAN
rs10882993	ZFYVE27	cis	cerebellum	SCAN
rs10882993	ZFYVE27	cis	parietal	SCAN
rs10882993	DHDPSL	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99497600-99522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99498000-99507800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:99498200-99507000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:99498200-99509000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:99498400-99514800	Strong transcription	Fetal Stomach	stomach
7	chr10:99498400-99517600	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr10:99498400-99519000	Strong transcription	Fetal Intestine Large	intestine
9	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr10:99498600-99514800	Strong transcription	Fetal Muscle Leg	muscle
11	chr10:99498600-99517800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr10:99498600-99518000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:99498600-99518000	Strong transcription	Fetal Thymus	thymus
14	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:99498600-99520600	Strong transcription	Osteobl	bone
16	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr10:99498600-99522400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:99498600-99522400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr10:99498600-99523000	Strong transcription	Thymus	Thymus
20	chr10:99498600-99523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:99498600-99524800	Weak transcription	Fetal Brain Male	brain
22	chr10:99498800-99506000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:99498800-99522400	Strong transcription	Dnd41	blood
24	chr10:99499000-99509600	Weak transcription	Psoas Muscle	Psoas
25	chr10:99499000-99517800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:99499000-99518000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:99499200-99505800	Strong transcription	HUVEC	blood vessel
28	chr10:99499200-99517000	Strong transcription	HSMM	muscle
29	chr10:99499200-99518000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:99499200-99522800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr10:99499200-99523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr10:99499400-99519000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:99499400-99522000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr10:99499400-99522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:99499600-99519200	Strong transcription	Placenta	Placenta
36	chr10:99499800-99505600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:99499800-99518000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr10:99500000-99523000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:99500200-99518000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:99500400-99522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr10:99500600-99506800	Weak transcription	Hela-S3	cervix
42	chr10:99500600-99523200	Strong transcription	Brain Germinal Matrix	brain
43	chr10:99500800-99507800	Weak transcription	Stomach Mucosa	stomach
44	chr10:99500800-99517800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:99500800-99518800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:99501000-99508000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:99501200-99517600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr10:99501600-99505600	Strong transcription	Colonic Mucosa	Colon
49	chr10:99501800-99517000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr10:99502000-99504800	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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