Variant report

Variant	rs1144895
Chromosome Location	chr7:65541307-65541308
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65540244..65541852-chr7:66118000..66119624,2	K562	blood:
2	chr7:65439470..65441298-chr7:65540371..65542201,2	K562	blood:
3	chr7:65540520..65541322-chrX:20159426..20159971,2	NB4	blood:
4	chr7:65536010..65538329-chr7:65539255..65541774,2	MCF-7	breast:
5	chr7:65538951..65542131-chr7:65578976..65581332,4	MCF-7	breast:
6	chr7:65540799..65542994-chr7:65578683..65581272,2	MCF-7	breast:
7	chr7:65540457..65542538-chr7:65550059..65552910,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126522	Chromatin interaction
ENSG00000173674	Chromatin interaction
ENSG00000249319	Chromatin interaction
ENSG00000241258	Chromatin interaction
ENSG00000205596	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000169919	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1144894	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1167395	0.84[AMR][1000 genomes]
rs1167406	0.81[AMR][1000 genomes]
rs1167411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1167612	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1182882	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1183245	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971949	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11974219	0.83[AMR][1000 genomes]
rs11974264	0.84[AMR][1000 genomes]
rs13225383	0.81[AMR][1000 genomes]
rs13240492	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13247295	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1540651	0.82[AMR][1000 genomes]
rs1565531	0.81[AMR][1000 genomes]
rs160635	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2087647	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2220626	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420168	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2460432	0.81[AMR][1000 genomes]
rs2949696	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35028832	0.81[AMR][1000 genomes]
rs427557	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs427575	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55962648	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6946143	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6957690	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6958484	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6961717	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs697968	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs697969	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs697970	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7801282	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs780742	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs780743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs780744	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs780998	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs809080	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875971	0.89[AMR][1000 genomes];0.84[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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv984546	chr7:65531382-65556631	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1144895	RP4-756H11.3	cis	Thyroid	GTEx
rs1144895	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs1144895	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs1144895	GS1-124K5.11	cis	Thyroid	GTEx
rs1144895	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1144895	RNU6-96P	cis	Thyroid	GTEx
rs1144895	GS1-124K5.4	cis	Artery Aorta	GTEx
rs1144895	RP4-756H11.3	cis	Artery Aorta	GTEx
rs1144895	GS1-124K5.4	cis	Stomach	GTEx
rs1144895	RP4-756H11.3	cis	lung	GTEx
rs1144895	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs1144895	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs1144895	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs1144895	RP4-756H11.3	cis	Artery Tibial	GTEx
rs1144895	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs1144895	GTF2IRD1P1	cis	Thyroid	GTEx
rs1144895	GS1-124K5.4	cis	Whole Blood	GTEx
rs1144895	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65540200-65541400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr7:65540200-65541400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:65540200-65541400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:65540200-65541400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr7:65540200-65541400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:65540200-65541400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr7:65540200-65541400	Active TSS	Brain Hippocampus Middle	brain
8	chr7:65540200-65541400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr7:65540200-65541400	Active TSS	Fetal Intestine Small	intestine
10	chr7:65540200-65541400	Active TSS	Rectal Smooth Muscle	rectum
11	chr7:65540200-65541400	Active TSS	Stomach Smooth Muscle	stomach
12	chr7:65540200-65541800	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr7:65540200-65542000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr7:65540200-65542000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:65540200-65542000	Active TSS	A549	lung
16	chr7:65540400-65541400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:65540400-65541400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:65540400-65541400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr7:65540400-65541400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:65540400-65541400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr7:65540400-65541400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:65540400-65541400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:65540400-65541400	Active TSS	Brain Substantia Nigra	brain
24	chr7:65540400-65541400	Active TSS	Lung	lung
25	chr7:65540400-65541400	Transcr. at gene 5' and 3'	Right Atrium	heart
26	chr7:65540400-65541400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr7:65540400-65541400	Active TSS	NHEK	skin
28	chr7:65540400-65541400	Active TSS	Osteobl	bone
29	chr7:65540400-65541600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr7:65540400-65541600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:65540400-65541600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:65540400-65541600	Active TSS	Aorta	Aorta
33	chr7:65540400-65541600	Active TSS	Gastric	stomach
34	chr7:65540400-65541600	Active TSS	Stomach Mucosa	stomach
35	chr7:65540400-65541800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:65540400-65542000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr7:65540400-65542000	Active TSS	Small Intestine	intestine
38	chr7:65540400-65542000	Active TSS	HSMM	muscle
39	chr7:65540400-65542200	Active TSS	Fetal Kidney	kidney
40	chr7:65540400-65542800	Active TSS	Fetal Intestine Large	intestine
41	chr7:65540600-65541400	Active TSS	K562	blood
42	chr7:65540600-65541400	Active TSS	NH-A	brain
43	chr7:65540600-65541600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:65540600-65541600	Active TSS	NHDF-Ad	bronchial
45	chr7:65540600-65542800	Active TSS	Liver	Liver
46	chr7:65540800-65541400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:65540800-65542400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:65541000-65541400	Flanking Active TSS	Placenta	Placenta
49	chr7:65541000-65541400	Flanking Active TSS	Thymus	Thymus
50	chr7:65541000-65541400	Flanking Active TSS	HSMMtube	muscle

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