Variant report

Variant	rs17142255
Chromosome Location	chr7:8075259-8075260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8006781..8009686-chr7:8074600..8077237,3	MCF-7	breast:
2	chr7:8065280..8067044-chr7:8073345..8076327,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12056007	0.81[AMR][1000 genomes]
rs16872351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16872488	0.81[CHB][hapmap];0.90[AMR][1000 genomes]
rs17141597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17141865	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17141876	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17142053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17142349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17142477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17142679	0.95[AMR][1000 genomes]
rs17142685	0.95[AMR][1000 genomes]
rs17142716	0.87[AMR][1000 genomes]
rs17142727	0.85[MEX][hapmap]
rs58145708	0.94[AMR][1000 genomes]
rs58348680	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58707745	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59427694	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59437461	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59697814	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60920460	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61351831	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62433384	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62433385	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62433405	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62433406	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62433407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62433408	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62433442	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62433444	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62433449	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62435365	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62435371	0.89[AMR][1000 genomes]
rs6463760	1.00[CEU][hapmap]
rs6955803	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs6956133	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs9640055	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]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv518779	chr7:8055664-8077359	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1793794	chr7:8064509-8078802	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17142255	CAPN2	trans	lymphoblastoid	seeQTL
rs17142255	MDK	trans	brain	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
2	chr7:8041600-8095000	Weak transcription	Gastric	stomach
3	chr7:8041800-8075400	Weak transcription	Brain Hippocampus Middle	brain
4	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:8047400-8075600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:8047600-8108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:8064400-8096200	Weak transcription	NHLF	lung
8	chr7:8065000-8076800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:8065000-8095000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:8065000-8108600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:8066400-8075600	Weak transcription	Fetal Kidney	kidney
12	chr7:8066400-8090800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:8066400-8096600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:8066400-8127600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:8066600-8077000	Weak transcription	Fetal Heart	heart
16	chr7:8066600-8082000	Weak transcription	Osteobl	bone
17	chr7:8066600-8099800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr7:8066800-8075400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:8066800-8075400	Weak transcription	Liver	Liver
21	chr7:8066800-8082600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:8066800-8091200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:8066800-8095000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:8066800-8095600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:8066800-8099800	Weak transcription	Brain Anterior Caudate	brain
26	chr7:8066800-8108600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:8067000-8078400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:8067000-8091800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
30	chr7:8067200-8075400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr7:8067200-8075800	Weak transcription	Fetal Intestine Large	intestine
32	chr7:8067200-8084000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:8067200-8095600	Weak transcription	Fetal Lung	lung
34	chr7:8067400-8082800	Weak transcription	Hela-S3	cervix
35	chr7:8067600-8076600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:8067600-8076600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:8067600-8095800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:8067800-8075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:8068000-8076800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:8068000-8095600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:8069800-8095800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:8074200-8075400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr7:8074200-8075600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:8074200-8076000	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr7:8074200-8076000	Genic enhancers	Fetal Thymus	thymus
46	chr7:8074200-8076200	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr7:8074200-8076200	ZNF genes & repeats	Fetal Brain Female	brain
48	chr7:8074200-8077200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:8074200-8077400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:8074200-8078400	Strong transcription	Dnd41	blood

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