Variant report

Variant	rs4368860
Chromosome Location	chr7:65608482-65608483
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65578534..65580943-chr7:65606200..65609199,3	MCF-7	breast:
2	chr7:65608461..65610824-chr7:65611925..65613549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10240249	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10253922	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10256544	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10268656	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10271553	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1129531	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1167390	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1167399	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1167406	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1167408	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1167612	0.83[AMR][1000 genomes]
rs11971949	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11974264	0.89[AFR][1000 genomes]
rs13240492	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13245728	0.92[AFR][1000 genomes]
rs13309935	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1540651	0.88[AFR][1000 genomes]
rs1612452	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1616988	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1976200	0.92[AFR][1000 genomes]
rs1983372	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2087647	0.85[AMR][1000 genomes]
rs2249458	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420168	0.83[AMR][1000 genomes]
rs2420173	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2420174	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2460430	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2460432	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28391294	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28470208	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2949696	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34550048	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35034167	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4612218	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718319	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718328	0.80[EUR][1000 genomes]
rs55962648	0.85[AMR][1000 genomes]
rs57866200	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59466412	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62467451	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6946143	0.85[AMR][1000 genomes]
rs6951787	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6957690	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6958484	0.85[AMR][1000 genomes]
rs6961717	0.86[AMR][1000 genomes]
rs6967708	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs709608	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs709609	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7782806	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7786892	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801282	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7809814	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs780998	0.81[AMR][1000 genomes]
rs875971	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs880166	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs908915	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9767916	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	nsv971489	chr7:65590579-65614004	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4368860	GS1-124K5.11	cis	Thyroid	GTEx
rs4368860	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs4368860	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs4368860	GS1-124K5.4	cis	Stomach	GTEx
rs4368860	RP4-756H11.3	cis	Thyroid	GTEx
rs4368860	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs4368860	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4368860	LINC00174	cis	Thyroid	GTEx
rs4368860	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs4368860	GS1-124K5.2	cis	Whole Blood	GTEx
rs4368860	RP4-756H11.3	cis	Artery Tibial	GTEx
rs4368860	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs4368860	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs4368860	GTF2IRD1P1	cis	Thyroid	GTEx
rs4368860	RNU6-96P	cis	Thyroid	GTEx
rs4368860	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs4368860	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs4368860	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:65590800-65613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:65594600-65610800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:65594800-65612200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:65594800-65614400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:65595000-65614400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr7:65595000-65614600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:65595000-65615200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:65595200-65613600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:65595200-65614000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:65595200-65622000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:65595600-65623200	Strong transcription	Dnd41	blood
13	chr7:65595600-65623800	Strong transcription	Primary T cells from cord blood	blood
14	chr7:65595800-65617200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:65595800-65620000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:65598800-65613600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:65599000-65612200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:65599200-65612200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr7:65599200-65612800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:65599200-65614200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:65599200-65623400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr7:65599600-65612800	Strong transcription	Primary hematopoietic stem cells	blood
23	chr7:65600400-65610800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:65601200-65611800	Strong transcription	Primary B cells from cord blood	blood
25	chr7:65602400-65611800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr7:65604200-65613400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:65604200-65614000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:65604400-65609200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:65604400-65609200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:65604400-65613800	Strong transcription	Fetal Thymus	thymus
31	chr7:65604600-65608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:65604600-65610600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:65604600-65610600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:65604600-65611600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr7:65604600-65613200	Strong transcription	Thymus	Thymus
36	chr7:65604600-65613600	Strong transcription	Brain Germinal Matrix	brain
37	chr7:65604600-65613800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:65604800-65612200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:65605200-65610600	Strong transcription	Hela-S3	cervix
40	chr7:65605800-65612600	Strong transcription	GM12878-XiMat	blood
41	chr7:65605800-65615200	Strong transcription	K562	blood
42	chr7:65606000-65609400	Strong transcription	NH-A	brain
43	chr7:65606000-65611400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr7:65606000-65613000	Strong transcription	A549	lung
45	chr7:65606200-65608600	Genic enhancers	Fetal Muscle Leg	muscle
46	chr7:65606200-65609400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr7:65606200-65609800	Strong transcription	Osteobl	bone
48	chr7:65606200-65610400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:65606200-65612400	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr7:65606200-65613000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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