Variant report

Variant	rs9640055
Chromosome Location	chr7:8029516-8029517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:8026444..8027944-chr7:8028522..8030290,2	MCF-7	breast:
2	chr7:8029061..8031816-chr7:8036537..8038816,2	K562	blood:
3	chr7:8024866..8028296-chr7:8029359..8032813,3	K562	blood:
4	chr7:8028828..8030747-chr7:8034985..8037908,2	MCF-7	breast:
5	chr7:8007363..8010547-chr7:8028829..8033493,5	MCF-7	breast:
6	chr7:8029120..8030983-chr7:8034331..8036288,2	K562	blood:
7	chr7:8008498..8010379-chr7:8028683..8031469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12056007	0.81[AMR][1000 genomes]
rs16872351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16872488	0.81[CHB][hapmap];0.90[AMR][1000 genomes]
rs17141597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17141865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17141876	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17142053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17142255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17142349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17142375	0.86[MEX][hapmap]
rs17142477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17142679	0.90[AMR][1000 genomes]
rs17142685	0.90[AMR][1000 genomes]
rs17142716	0.83[AMR][1000 genomes]
rs58145708	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58348680	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58707745	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59427694	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59437461	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59697814	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60920460	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61351831	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62433384	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62433385	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62433405	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62433406	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62433407	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62433408	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62433442	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62433444	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62433449	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6463760	1.00[CEU][hapmap]
rs6955803	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs6956133	1.00[CEU][hapmap];0.93[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9640055	MDK	trans	brain	seeQTL
rs9640055	CD99	trans	brain	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8013400-8029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:8015200-8031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:8017800-8029600	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:8017800-8029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:8019000-8031400	Weak transcription	Primary B cells from cord blood	blood
7	chr7:8025000-8029600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:8025000-8031600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:8026400-8031000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:8027600-8034800	Weak transcription	Fetal Thymus	thymus
11	chr7:8028600-8029600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:8028600-8030000	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr7:8028600-8030000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:8028800-8029800	Flanking Active TSS	Dnd41	blood
15	chr7:8028800-8030000	Enhancers	Brain Germinal Matrix	brain
16	chr7:8028800-8030000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr7:8029000-8029600	Active TSS	GM12878-XiMat	blood
18	chr7:8029000-8029600	Enhancers	Hela-S3	cervix
19	chr7:8029000-8029800	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr7:8029000-8029800	Active TSS	Right Atrium	heart
21	chr7:8029000-8029800	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr7:8029000-8030000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:8029000-8030000	Enhancers	Stomach Mucosa	stomach
24	chr7:8029000-8030400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr7:8029000-8039000	Weak transcription	Thymus	Thymus
26	chr7:8029200-8029600	Active TSS	Primary hematopoietic stem cells	blood
27	chr7:8029200-8029600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr7:8029200-8029600	Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr7:8029200-8029600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:8029200-8029600	Active TSS	Osteobl	bone
31	chr7:8029200-8029800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr7:8029200-8029800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:8029200-8029800	Enhancers	Brain Anterior Caudate	brain
34	chr7:8029200-8029800	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr7:8029200-8030000	Active TSS	Primary T cells fromperipheralblood	blood
36	chr7:8029200-8030000	Active TSS	Stomach Smooth Muscle	stomach
37	chr7:8029200-8030000	Active TSS	K562	blood
38	chr7:8029200-8043600	Weak transcription	Small Intestine	intestine
39	chr7:8029400-8029600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr7:8029400-8029600	Enhancers	Fetal Heart	heart
41	chr7:8029400-8029800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:8029400-8029800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr7:8029400-8029800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:8029400-8029800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr7:8029400-8029800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:8029400-8029800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr7:8029400-8029800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:8029400-8029800	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr7:8029400-8029800	Flanking Active TSS	Liver	Liver
50	chr7:8029400-8029800	Enhancers	Brain Cingulate Gyrus	brain

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