Variant report

Variant	rs4917784
Chromosome Location	chr10:99502430-99502431
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99496561..99499053-chr10:99501574..99505641,4	MCF-7	breast:
2	chr10:99424940..99426723-chr10:99501991..99504090,2	K562	blood:
3	chr10:99500710..99504055-chr10:99516731..99520441,4	K562	blood:
4	chr10:99445609..99447158-chr10:99500562..99503071,2	MCF-7	breast:
5	chr10:99494917..99500697-chr10:99501380..99508176,12	K562	blood:

Variant related genes	Relation type
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10748707	0.96[CEU][hapmap]
rs10748708	0.83[ASN][1000 genomes]
rs10786367	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10786368	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10786369	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10786370	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10786371	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10786372	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10882993	0.83[JPT][hapmap]
rs10882995	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10882996	0.87[ASN][1000 genomes]
rs11189350	0.97[ASN][1000 genomes]
rs11189352	0.91[ASN][1000 genomes]
rs11189353	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11189355	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11189356	0.91[ASN][1000 genomes]
rs11189357	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11189359	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11189360	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs11189367	0.82[ASN][1000 genomes]
rs11189374	0.80[ASN][1000 genomes]
rs11189376	0.80[ASN][1000 genomes]
rs11591898	0.94[ASN][1000 genomes]
rs11597378	0.94[CHB][hapmap]
rs12412543	0.87[ASN][1000 genomes]
rs1253023	0.81[AMR][1000 genomes]
rs1253027	0.80[MEX][hapmap]
rs12569711	0.87[ASN][1000 genomes]
rs1538723	0.93[ASN][1000 genomes]
rs1981237	0.82[JPT][hapmap]
rs1981238	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2039826	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3750612	0.83[JPT][hapmap]
rs3750614	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3750615	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3814558	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3814559	0.81[JPT][hapmap]
rs3814560	0.82[JPT][hapmap]
rs3818876	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3829137	0.80[MEX][hapmap]
rs4244329	0.82[JPT][hapmap]
rs4244330	0.83[ASN][1000 genomes]
rs4593946	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs4917783	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4917785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7080894	0.82[JPT][hapmap]
rs7080953	0.81[JPT][hapmap]
rs7081361	0.82[ASN][1000 genomes]
rs7099540	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7100453	0.80[ASN][1000 genomes]
rs7478323	0.83[ASN][1000 genomes]
rs7907679	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7916454	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7922907	0.85[JPT][hapmap]
rs883324	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs946777	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs946778	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs946779	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs946780	0.88[CEU][hapmap];0.87[MEX][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4917784	LZTS2	cis	cerebellum	SCAN
rs4917784	MARVELD1	cis	lung	GTEx
rs4917784	ZFYVE27	cis	parietal	SCAN
rs4917784	FBXW4	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr10:99498200-99502600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:99498200-99503600	Strong transcription	Fetal Lung	lung
5	chr10:99498200-99507000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:99498200-99509000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:99498400-99502600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:99498400-99504000	Weak transcription	Small Intestine	intestine
10	chr10:99498400-99514800	Strong transcription	Fetal Stomach	stomach
11	chr10:99498400-99517600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr10:99498400-99519000	Strong transcription	Fetal Intestine Large	intestine
13	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr10:99498600-99502600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:99498600-99502600	Strong transcription	Liver	Liver
16	chr10:99498600-99502600	Weak transcription	Brain Angular Gyrus	brain
17	chr10:99498600-99502600	Weak transcription	Brain Substantia Nigra	brain
18	chr10:99498600-99502600	Weak transcription	Gastric	stomach
19	chr10:99498600-99502600	Strong transcription	NHEK	skin
20	chr10:99498600-99502800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:99498600-99502800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:99498600-99502800	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:99498600-99502800	Weak transcription	Right Atrium	heart
24	chr10:99498600-99504400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr10:99498600-99514800	Strong transcription	Fetal Muscle Leg	muscle
26	chr10:99498600-99517800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:99498600-99518000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr10:99498600-99518000	Strong transcription	Fetal Thymus	thymus
29	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:99498600-99520600	Strong transcription	Osteobl	bone
31	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr10:99498600-99522400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr10:99498600-99522400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr10:99498600-99523000	Strong transcription	Thymus	Thymus
35	chr10:99498600-99523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr10:99498600-99524800	Weak transcription	Fetal Brain Male	brain
37	chr10:99498800-99502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:99498800-99506000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:99498800-99522400	Strong transcription	Dnd41	blood
40	chr10:99499000-99509600	Weak transcription	Psoas Muscle	Psoas
41	chr10:99499000-99517800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:99499000-99518000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:99499200-99505800	Strong transcription	HUVEC	blood vessel
44	chr10:99499200-99517000	Strong transcription	HSMM	muscle
45	chr10:99499200-99518000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:99499200-99522800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr10:99499200-99523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:99499400-99519000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:99499400-99522000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr10:99499400-99522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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