Variant report

Variant	rs2460427
Chromosome Location	chr7:65619205-65619206
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	chr7:65617048..65619822-chr7:65625013..65626809,2	MCF-7	breast:
2	chr7:65446691..65448444-chr7:65618479..65620177,2	K562	blood:

Variant related genes	Relation type
ENSG00000169919	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10950024	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950027	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10950028	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10950029	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11760805	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11767833	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12666485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12671834	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12673308	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs160636	0.81[ASN][1000 genomes]
rs160640	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs160641	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs160645	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs160647	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17138089	0.89[ASN][1000 genomes]
rs17138149	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs221986	0.89[ASN][1000 genomes]
rs2451953	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2465121	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28815324	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2946580	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313817	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs313818	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313823	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313828	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs313830	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs316305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316316	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316320	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316323	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316328	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs400767	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4441996	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718325	0.85[ASN][1000 genomes]
rs6460276	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460281	0.86[ASN][1000 genomes]
rs67302640	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67397473	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67688847	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67775320	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6960870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73136346	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73142233	0.85[ASN][1000 genomes]
rs73142245	0.85[ASN][1000 genomes]
rs73376394	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73376401	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73378304	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7782212	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783727	0.80[ASN][1000 genomes]
rs7786728	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7786735	0.84[ASN][1000 genomes]
rs7787063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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	nsv971172	chr7:65616238-65653268	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2460427	GTF2IRD1P1	cis	Thyroid	GTEx
rs2460427	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2460427	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2460427	GS1-124K5.11	cis	Thyroid	GTEx
rs2460427	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs2460427	GS1-124K5.4	cis	Stomach	GTEx
rs2460427	RNU6-96P	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65595200-65622000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:65595600-65623200	Strong transcription	Dnd41	blood
3	chr7:65595600-65623800	Strong transcription	Primary T cells from cord blood	blood
4	chr7:65595800-65620000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:65599200-65623400	Strong transcription	Primary B cells from peripheral blood	blood
6	chr7:65609000-65622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:65609200-65623200	Weak transcription	Fetal Brain Male	brain
8	chr7:65609200-65623400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:65609600-65624600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:65612000-65635400	Weak transcription	Fetal Kidney	kidney
11	chr7:65613600-65621600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:65614200-65620000	Strong transcription	GM12878-XiMat	blood
13	chr7:65615200-65622600	Strong transcription	Fetal Brain Female	brain
14	chr7:65615200-65623400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:65615200-65623800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:65615200-65623800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr7:65615400-65619400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr7:65615400-65619600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:65615400-65623600	Strong transcription	Primary B cells from cord blood	blood
20	chr7:65615400-65623600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:65615400-65623800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:65615600-65619400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr7:65615600-65619600	Strong transcription	Thymus	Thymus
24	chr7:65615600-65624000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:65615800-65621000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:65615800-65621800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:65615800-65621800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:65615800-65623800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:65615800-65624000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:65616000-65620000	Strong transcription	HSMM	muscle
31	chr7:65616000-65623200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:65616000-65623800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:65616200-65619400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr7:65616200-65619400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr7:65616200-65619600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr7:65616200-65623400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:65616200-65623400	Strong transcription	Fetal Thymus	thymus
38	chr7:65616200-65624400	Weak transcription	Psoas Muscle	Psoas
39	chr7:65616400-65623600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:65616600-65619400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:65616600-65619400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr7:65616800-65619400	Strong transcription	HSMMtube	muscle
43	chr7:65617000-65619400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr7:65617200-65619400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:65617200-65623800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:65617400-65620000	Strong transcription	Brain Angular Gyrus	brain
47	chr7:65617600-65628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:65617600-65632400	Weak transcription	Hela-S3	cervix
49	chr7:65617800-65619400	Strong transcription	Brain Anterior Caudate	brain
50	chr7:65617800-65619400	Strong transcription	Brain Cingulate Gyrus	brain

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