Variant report

Variant	rs2460431
Chromosome Location	chr7:65622846-65622847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65540658..65542432-chr7:65622209..65624155,2	K562	blood:
2	chr7:65611050..65612887-chr7:65620053..65622926,2	K562	blood:

Variant related genes	Relation type
ENSG00000126522	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs10247526	0.90[EUR][1000 genomes]
rs1061361	0.80[AMR][1000 genomes]
rs10807699	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10807701	0.91[EUR][1000 genomes]
rs10807702	0.91[EUR][1000 genomes]
rs10950032	0.91[EUR][1000 genomes]
rs12530490	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12667373	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13308751	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1392104	0.91[EUR][1000 genomes]
rs1499613	0.91[EUR][1000 genomes]
rs1499614	0.91[EUR][1000 genomes]
rs1532573	0.91[EUR][1000 genomes]
rs1546059	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1553174	0.91[EUR][1000 genomes]
rs160543	0.93[AMR][1000 genomes]
rs160637	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs160638	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs160639	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs160642	0.93[AMR][1000 genomes]
rs160643	0.93[AMR][1000 genomes]
rs160644	0.93[AMR][1000 genomes]
rs160646	0.93[AMR][1000 genomes]
rs160648	0.87[AMR][1000 genomes]
rs160649	0.87[AMR][1000 genomes]
rs160651	0.87[AMR][1000 genomes]
rs160652	0.89[AMR][1000 genomes]
rs160655	0.87[AMR][1000 genomes]
rs160656	0.94[AMR][1000 genomes]
rs160657	0.94[AMR][1000 genomes]
rs1715235	0.80[AMR][1000 genomes]
rs1723266	0.80[AMR][1000 genomes]
rs1723267	0.80[AMR][1000 genomes]
rs1723269	0.80[AMR][1000 genomes]
rs1723270	0.80[AMR][1000 genomes]
rs182600	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs186378	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1873494	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs188765	0.80[AMR][1000 genomes]
rs1964692	0.80[AMR][1000 genomes]
rs1979823	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2243480	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2257790	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2420170	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2420171	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420172	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460422	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2460425	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460426	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2637561	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2658583	0.80[AMR][1000 genomes]
rs2961102	0.80[AMR][1000 genomes]
rs3105600	0.80[AMR][1000 genomes]
rs313798	0.80[AMR][1000 genomes]
rs313801	0.85[AMR][1000 genomes]
rs313802	0.85[AMR][1000 genomes]
rs313803	0.85[AMR][1000 genomes]
rs313809	0.80[AMR][1000 genomes]
rs313813	0.82[AMR][1000 genomes]
rs313814	0.82[AMR][1000 genomes]
rs313819	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs313820	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs313822	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs313824	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs313831	0.94[AMR][1000 genomes]
rs313832	0.93[AMR][1000 genomes]
rs313833	0.93[AMR][1000 genomes]
rs316304	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316307	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316313	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs316314	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316315	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs316317	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316318	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316321	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316322	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316325	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316326	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316327	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316329	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316331	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316332	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs316333	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs316334	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34032527	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34970380	0.80[AMR][1000 genomes]
rs35396113	0.80[AMR][1000 genomes]
rs36084489	0.80[AMR][1000 genomes]
rs36127118	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs383402	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs387676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs392355	0.80[AMR][1000 genomes]
rs402418	0.82[AMR][1000 genomes]
rs403089	0.85[AMR][1000 genomes]
rs4145008	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4149468	0.90[EUR][1000 genomes]
rs419603	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs422164	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs423187	0.80[AMR][1000 genomes]
rs4236207	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs427044	0.80[AMR][1000 genomes]
rs431076	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs431318	0.82[AMR][1000 genomes]
rs437889	0.82[AMR][1000 genomes]
rs4481472	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs448377	0.80[AMR][1000 genomes]
rs451396	0.80[AMR][1000 genomes]
rs458291	0.84[AMR][1000 genomes]
rs462853	0.93[AMR][1000 genomes]
rs465359	0.93[AMR][1000 genomes]
rs466983	0.84[AMR][1000 genomes]
rs4718309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718315	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718316	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718317	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718333	0.90[EUR][1000 genomes]
rs59966766	0.80[AMR][1000 genomes]
rs6460274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6460277	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6460285	0.81[EUR][1000 genomes]
rs6958289	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6958420	0.91[EUR][1000 genomes]
rs6959002	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6964245	0.91[EUR][1000 genomes]
rs6964530	0.84[EUR][1000 genomes]
rs6966322	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6974723	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73136349	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73148097	0.80[AMR][1000 genomes]
rs73150014	0.80[AMR][1000 genomes]
rs7778911	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778679	0.88[EUR][1000 genomes]
rs778683	0.85[EUR][1000 genomes]
rs778687	0.91[EUR][1000 genomes]
rs7787230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778729	0.91[EUR][1000 genomes]
rs778732	0.85[EUR][1000 genomes]
rs778733	0.91[EUR][1000 genomes]
rs7792391	0.90[EUR][1000 genomes]
rs7804223	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs780453	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7808834	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs781150	0.80[AMR][1000 genomes]
rs781153	0.80[AMR][1000 genomes]
rs781154	0.80[AMR][1000 genomes]
rs781155	0.80[AMR][1000 genomes]
rs781156	0.80[AMR][1000 genomes]
rs958550	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9769882	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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
rs2460431	GUSB	cis	Whole Blood	GTEx
rs2460431	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2460431	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2460431	VKORC1L1	cis	Whole Blood	GTEx
rs2460431	RP4-756H11.3	cis	lung	GTEx
rs2460431	ASL	cis	multi-tissue	Pritchard
rs2460431	ASL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65595600-65623200	Strong transcription	Dnd41	blood
2	chr7:65595600-65623800	Strong transcription	Primary T cells from cord blood	blood
3	chr7:65599200-65623400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr7:65609200-65623200	Weak transcription	Fetal Brain Male	brain
5	chr7:65609200-65623400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:65609600-65624600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:65612000-65635400	Weak transcription	Fetal Kidney	kidney
8	chr7:65615200-65623400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr7:65615200-65623800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:65615200-65623800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr7:65615400-65623600	Strong transcription	Primary B cells from cord blood	blood
12	chr7:65615400-65623600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:65615400-65623800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:65615600-65624000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:65615800-65623800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:65615800-65624000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:65616000-65623200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:65616000-65623800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:65616200-65623400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:65616200-65623400	Strong transcription	Fetal Thymus	thymus
21	chr7:65616200-65624400	Weak transcription	Psoas Muscle	Psoas
22	chr7:65616400-65623600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:65617200-65623800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:65617600-65628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:65617600-65632400	Weak transcription	Hela-S3	cervix
26	chr7:65617800-65623800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:65618000-65623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:65618000-65623000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:65618000-65623800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:65618000-65624600	Strong transcription	Fetal Muscle Leg	muscle
31	chr7:65618200-65623000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr7:65618200-65623200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr7:65618200-65623200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:65618200-65623600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:65618200-65623600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:65618200-65623800	Strong transcription	Osteobl	bone
37	chr7:65618200-65624000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr7:65618200-65624200	Strong transcription	Fetal Lung	lung
39	chr7:65618200-65625200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr7:65618200-65632400	Weak transcription	HUVEC	blood vessel
41	chr7:65618200-65635400	Weak transcription	Esophagus	oesophagus
42	chr7:65618200-65635600	Weak transcription	Right Ventricle	heart
43	chr7:65618400-65623200	Weak transcription	Colonic Mucosa	Colon
44	chr7:65618400-65623800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:65618400-65623800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:65618400-65624400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:65618800-65624800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr7:65618800-65625400	Weak transcription	Fetal Heart	heart
49	chr7:65618800-65627600	Weak transcription	NHEK	skin
50	chr7:65619000-65625000	Weak transcription	H1 Cell Line	embryonic stem cell

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