Variant report

Variant	rs3757417
Chromosome Location	chr7:65825257-65825258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65821519..65823767-chr7:65824907..65826814,2	MCF-7	breast:
2	chr7:65819420..65821151-chr7:65824065..65825748,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRCP-3	chr7:65824882-65825437	NONHSAT121146

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10081172	0.83[CHB][hapmap];0.92[CHD][hapmap];0.82[EUR][1000 genomes]
rs10236665	0.84[EUR][1000 genomes]
rs10264619	0.85[EUR][1000 genomes]
rs10275413	0.84[EUR][1000 genomes]
rs16868546	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs17138154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1862086	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1895134	0.82[EUR][1000 genomes]
rs2420598	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28455065	0.82[EUR][1000 genomes]
rs28606020	0.84[EUR][1000 genomes]
rs4149463	1.00[ASW][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[ASN][1000 genomes]
rs4587218	0.83[EUR][1000 genomes]
rs58123804	0.83[EUR][1000 genomes]
rs58973756	0.83[EUR][1000 genomes]
rs61132090	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6949083	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73144219	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73148698	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73152719	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3757417	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs3757417	GS1-124K5.12	cis	Artery Tibial	GTEx
rs3757417	C7orf42	cis	cerebellum	SCAN
rs3757417	GS1-124K5.12	cis	lung	GTEx
rs3757417	CRCP	cis	parietal	SCAN
rs3757417	ZNF273	cis	parietal	SCAN
rs3757417	CRCP	cis	cerebellum	SCAN
rs3757417	GUSB	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65805200-65843600	Weak transcription	Aorta	Aorta
2	chr7:65814000-65843800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:65817000-65843400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:65817400-65825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:65817400-65842600	Weak transcription	Gastric	stomach
6	chr7:65817600-65826600	Weak transcription	Left Ventricle	heart
7	chr7:65817600-65828800	Weak transcription	Ovary	ovary
8	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
11	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
12	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:65819800-65826400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr7:65821400-65825600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:65821600-65825600	Weak transcription	HSMMtube	muscle
17	chr7:65821800-65826000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:65822000-65831800	Weak transcription	HSMM	muscle
19	chr7:65822000-65843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:65822200-65828800	Weak transcription	Osteobl	bone
21	chr7:65822400-65831400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:65822400-65831400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:65822600-65827400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:65822800-65839200	Weak transcription	Fetal Intestine Small	intestine
25	chr7:65822800-65841200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:65823400-65825400	Flanking Active TSS	HMEC	breast
27	chr7:65823400-65826400	Strong transcription	Liver	Liver
28	chr7:65823400-65843600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:65823600-65826200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:65824000-65831200	Weak transcription	Fetal Lung	lung
31	chr7:65824200-65826400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:65824200-65826400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:65824400-65825600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:65824400-65826200	Flanking Active TSS	NHEK	skin
35	chr7:65824600-65826600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:65824800-65827400	Weak transcription	HepG2	liver
37	chr7:65824800-65843600	Weak transcription	Esophagus	oesophagus
38	chr7:65825000-65825600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:65825000-65825800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:65825000-65826000	Weak transcription	Placenta	Placenta
41	chr7:65825000-65826800	Strong transcription	Fetal Stomach	stomach
42	chr7:65825000-65828800	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:65825000-65833800	Weak transcription	Fetal Muscle Leg	muscle
44	chr7:65825000-65844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:65825200-65826600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:65825200-65826800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:65825200-65827200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:65825200-65827400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:65825200-65827400	Weak transcription	Lung	lung
50	chr7:65825200-65831200	Weak transcription	NHDF-Ad	bronchial

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