Variant report

Variant	rs9462240
Chromosome Location	chr6:36870613-36870614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36867430..36871951-chr6:36875008..36877997,4	K562	blood:
2	chr6:36868611..36871179-chr6:36873388..36875751,3	K562	blood:
3	chr6:36852943..36861433-chr6:36865588..36872573,10	K562	blood:
4	chr6:36560719..36562370-chr6:36870379..36872149,2	K562	blood:
5	chr6:36852581..36854443-chr6:36870152..36872140,2	K562	blood:

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1022696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10456446	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1046578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10498736	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947638	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10947639	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10947640	1.00[CEU][hapmap];0.84[CHB][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947645	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11757380	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11759850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11963298	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11970506	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12110889	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12193721	0.82[EUR][1000 genomes]
rs12194154	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12202755	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12213087	0.90[GIH][hapmap]
rs12213912	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13199306	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16889252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272276	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280675	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293392	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2395663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3734331	0.91[ASN][1000 genomes]
rs3734333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3957238	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4475317	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711473	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711474	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4714023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59892114	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60992755	0.83[ASN][1000 genomes]
rs6457964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67854134	0.87[ASN][1000 genomes]
rs6901884	0.94[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6904504	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910832	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs6920322	0.84[ASN][1000 genomes]
rs6932038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6932175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6934844	0.93[LWK][hapmap];0.84[YRI][hapmap]
rs7741378	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7757241	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7761425	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7761653	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7770155	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7774420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380616	0.88[YRI][hapmap]
rs9380618	0.83[LWK][hapmap];0.85[YRI][hapmap]
rs9462238	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9462239	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470426	0.81[YRI][hapmap]
rs9470434	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470439	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9918461	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9969040	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs997674	0.85[JPT][hapmap];0.81[ASN][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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9462240	C6orf1	cis	parietal	SCAN
rs9462240	PNPLA1	cis	parietal	SCAN
rs9462240	C6orf89	cis	parietal	SCAN
rs9462240	NUDT3	cis	cerebellum	SCAN
rs9462240	C6orf89	cis	cerebellum	SCAN
rs9462240	KCNK16	cis	parietal	SCAN
rs9462240	SFRS3	cis	lymphoblastoid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36873600	Weak transcription	Aorta	Aorta
2	chr6:36854200-36881000	Weak transcription	Gastric	stomach
3	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:36854800-36875200	Weak transcription	Esophagus	oesophagus
6	chr6:36854800-36881000	Weak transcription	A549	lung
7	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:36855400-36881000	Weak transcription	Small Intestine	intestine
10	chr6:36857000-36874400	Weak transcription	Pancreas	Pancrea
11	chr6:36859600-36879400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:36861200-36879000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr6:36862000-36875800	Strong transcription	Dnd41	blood
14	chr6:36864600-36871800	Strong transcription	Fetal Stomach	stomach
15	chr6:36864600-36881200	Strong transcription	Fetal Intestine Small	intestine
16	chr6:36865400-36873200	Strong transcription	Primary T cells from cord blood	blood
17	chr6:36865400-36874200	Strong transcription	Fetal Muscle Leg	muscle
18	chr6:36865400-36876600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:36865600-36871200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:36866000-36871600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:36866000-36875800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:36866000-36876800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:36866000-36877200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:36866200-36874200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr6:36866200-36876800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:36866200-36877600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr6:36866200-36878400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:36866400-36877800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:36866600-36871000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:36866600-36871200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr6:36866600-36876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:36866600-36876200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:36866600-36878400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:36866600-36878400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:36866800-36872600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:36866800-36874400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:36866800-36876000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:36866800-36881600	Strong transcription	Fetal Intestine Large	intestine
40	chr6:36867000-36874400	Strong transcription	Thymus	Thymus
41	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:36867200-36872200	Strong transcription	NHDF-Ad	bronchial
43	chr6:36867200-36873000	Weak transcription	Fetal Heart	heart
44	chr6:36867400-36871400	Strong transcription	Fetal Thymus	thymus
45	chr6:36867800-36872600	Weak transcription	Spleen	Spleen
46	chr6:36868400-36871400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:36868600-36871800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:36868600-36872200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:36868600-36882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:36869000-36871800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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