Variant report

Variant	rs778731
Chromosome Location	chr7:65823015-65823016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65821519..65823767-chr7:65824907..65826814,2	MCF-7	breast:
2	chr7:65578221..65580076-chr7:65821592..65823424,2	K562	blood:
3	chr7:65793897..65795825-chr7:65821186..65823238,2	K562	blood:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1002053	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10215948	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10257427	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10267430	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11765965	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13227219	0.89[ASN][1000 genomes]
rs1643395	0.82[ASN][1000 genomes]
rs1695815	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1968225	0.84[ASN][1000 genomes]
rs2036264	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2173570	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3935391	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4718343	0.84[ASN][1000 genomes]
rs4718344	0.84[ASN][1000 genomes]
rs55748098	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460291	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460292	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460295	0.81[ASN][1000 genomes]
rs6945843	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6949920	0.80[ASN][1000 genomes]
rs6956179	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6960476	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6971509	0.82[EUR][1000 genomes]
rs6979382	0.81[ASN][1000 genomes]
rs709595	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs709597	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7783613	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778682	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778685	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778689	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778692	0.84[ASN][1000 genomes]
rs778694	0.84[ASN][1000 genomes]
rs778695	0.82[ASN][1000 genomes]
rs778699	0.84[ASN][1000 genomes]
rs778700	0.84[ASN][1000 genomes]
rs778706	0.85[ASN][1000 genomes]
rs778708	0.86[ASN][1000 genomes]
rs778710	0.86[ASN][1000 genomes]
rs778712	0.88[ASN][1000 genomes]
rs778721	0.86[ASN][1000 genomes]
rs778723	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778726	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778727	0.87[ASN][1000 genomes]
rs778735	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7791891	0.85[ASN][1000 genomes]
rs7794930	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7803424	0.81[ASN][1000 genomes]
rs937495	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9969301	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs778731	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs778731	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs778731	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs778731	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs778731	RP4-756H11.3	cis	Artery Aorta	GTEx
rs778731	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs778731	GS1-124K5.4	cis	Stomach	GTEx
rs778731	TPST1	cis	Thyroid	GTEx
rs778731	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs778731	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs778731	RP4-756H11.3	cis	Thyroid	GTEx
rs778731	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs778731	RP4-756H11.3	cis	Artery Tibial	GTEx
rs778731	RNU6-96P	cis	Thyroid	GTEx
rs778731	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:58 , 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	chr7:65814200-65823800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr7:65815000-65824600	Weak transcription	Lung	lung
5	chr7:65817000-65843400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:65817200-65824400	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:65817400-65823600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:65817400-65823800	Weak transcription	Spleen	Spleen
9	chr7:65817400-65824600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:65817400-65825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:65817400-65842600	Weak transcription	Gastric	stomach
12	chr7:65817600-65823600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:65817600-65824600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:65817600-65826600	Weak transcription	Left Ventricle	heart
15	chr7:65817600-65828800	Weak transcription	Ovary	ovary
16	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
17	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
19	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
20	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:65818400-65824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:65819200-65823400	Weak transcription	Liver	Liver
23	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:65819400-65823400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:65819800-65826400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr7:65821000-65824000	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:65821200-65825200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:65821400-65823400	Active TSS	HMEC	breast
29	chr7:65821400-65824400	Weak transcription	Placenta	Placenta
30	chr7:65821400-65825600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr7:65821600-65825600	Weak transcription	HSMMtube	muscle
32	chr7:65821800-65823400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:65821800-65824600	Weak transcription	NHDF-Ad	bronchial
34	chr7:65821800-65826000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr7:65822000-65824200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr7:65822000-65831800	Weak transcription	HSMM	muscle
37	chr7:65822000-65843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:65822200-65828800	Weak transcription	Osteobl	bone
39	chr7:65822400-65823600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:65822400-65823800	Weak transcription	Esophagus	oesophagus
41	chr7:65822400-65831400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:65822400-65831400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:65822600-65823200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr7:65822600-65823400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:65822600-65823600	Weak transcription	Fetal Lung	lung
46	chr7:65822600-65823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:65822600-65823800	Weak transcription	Fetal Stomach	stomach
48	chr7:65822600-65824600	Weak transcription	NHLF	lung
49	chr7:65822600-65827400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:65822800-65823600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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