Variant report

Variant	rs7907679
Chromosome Location	chr10:99500480-99500481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99499187..99502135-chr10:99502777..99505222,2	MCF-7	breast:
2	chr10:99500286..99501793-chr10:99503721..99505250,2	MCF-7	breast:
3	chr10:99498531..99500658-chr10:99522129..99523700,2	K562	blood:
4	chr10:99496240..99498427-chr10:99498501..99501523,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10748708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786367	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786371	0.90[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs10786372	0.95[CEU][hapmap];0.83[JPT][hapmap]
rs10882993	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]
rs10882994	0.80[EUR][1000 genomes]
rs10882995	0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs10882998	0.86[CHB][hapmap]
rs11189350	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11189352	0.83[EUR][1000 genomes]
rs11189353	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11189355	0.80[JPT][hapmap]
rs11189357	0.85[JPT][hapmap]
rs11189359	0.84[CHD][hapmap]
rs11189360	0.85[CEU][hapmap]
rs11189361	0.83[ASN][1000 genomes]
rs11189362	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1253027	0.84[CHD][hapmap]
rs1981237	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs1981238	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs2027376	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2039826	0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs3750612	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750614	0.95[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs3750615	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs3814558	0.95[CEU][hapmap];0.84[JPT][hapmap]
rs3814559	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs3814560	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs4244329	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs4917784	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4917785	0.83[ASN][1000 genomes]
rs4919139	0.87[CHB][hapmap]
rs7077725	0.85[ASN][1000 genomes]
rs7080894	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7080953	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs7099540	0.85[CEU][hapmap]
rs7916164	0.85[ASN][1000 genomes]
rs7916454	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs7916593	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7922907	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs883324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946777	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs946778	0.95[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.86[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7907679	MARVELD1	cis	lung	GTEx
rs7907679	MIR1287	cis	lymphoblastoid	seeQTL
rs7907679	ZFYVE27	cis	parietal	SCAN
rs7907679	ZFYVE27	cis	cerebellum	SCAN
rs7907679	DHDPSL	cis	cerebellum	SCAN

Chromatin state (count:127 , 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	chr10:99498000-99501000	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr10:99498000-99502000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:99498000-99507800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:99498200-99500800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:99498200-99501000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:99498200-99502600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:99498200-99503600	Strong transcription	Fetal Lung	lung
9	chr10:99498200-99507000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr10:99498200-99509000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:99498400-99500600	Genic enhancers	HepG2	liver
13	chr10:99498400-99501000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr10:99498400-99501600	Weak transcription	Colonic Mucosa	Colon
15	chr10:99498400-99502000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:99498400-99502600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr10:99498400-99504000	Weak transcription	Small Intestine	intestine
18	chr10:99498400-99514800	Strong transcription	Fetal Stomach	stomach
19	chr10:99498400-99517600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr10:99498400-99519000	Strong transcription	Fetal Intestine Large	intestine
21	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr10:99498600-99500600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:99498600-99500800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr10:99498600-99500800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:99498600-99500800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr10:99498600-99501000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:99498600-99501600	Weak transcription	Spleen	Spleen
28	chr10:99498600-99502000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:99498600-99502000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:99498600-99502000	Weak transcription	Aorta	Aorta
31	chr10:99498600-99502000	Weak transcription	Esophagus	oesophagus
32	chr10:99498600-99502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:99498600-99502600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:99498600-99502600	Strong transcription	Liver	Liver
35	chr10:99498600-99502600	Weak transcription	Brain Angular Gyrus	brain
36	chr10:99498600-99502600	Weak transcription	Brain Substantia Nigra	brain
37	chr10:99498600-99502600	Weak transcription	Gastric	stomach
38	chr10:99498600-99502600	Strong transcription	NHEK	skin
39	chr10:99498600-99502800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:99498600-99502800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:99498600-99502800	Weak transcription	Colon Smooth Muscle	Colon
42	chr10:99498600-99502800	Weak transcription	Right Atrium	heart
43	chr10:99498600-99504400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr10:99498600-99514800	Strong transcription	Fetal Muscle Leg	muscle
45	chr10:99498600-99517800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:99498600-99518000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:99498600-99518000	Strong transcription	Fetal Thymus	thymus
48	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr10:99498600-99520600	Strong transcription	Osteobl	bone
50	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum

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