Variant report

Variant	rs9462241
Chromosome Location	chr6:36870751-36870752
allele	A/T
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	chr6:36860505..36863428-chr6:36870664..36872408,2	MCF-7	breast:
4	chr6:36852943..36861433-chr6:36865588..36872573,10	K562	blood:
5	chr6:36560719..36562370-chr6:36870379..36872149,2	K562	blood:
6	chr6:36852581..36854443-chr6:36870152..36872140,2	K562	blood:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1022696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10456446	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1046578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10498736	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10947638	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947639	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947640	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947645	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757380	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11759850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11963298	1.00[CEU][hapmap];0.84[CHB][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];0.93[ASN][1000 genomes]
rs12193721	0.82[EUR][1000 genomes]
rs12194154	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12202755	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12213912	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13199306	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16889252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2272275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272276	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[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];0.94[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];0.87[ASN][1000 genomes]
rs2395663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3734331	0.92[ASN][1000 genomes]
rs3734333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3957238	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4475317	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711473	0.88[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];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59892114	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60992755	0.84[ASN][1000 genomes]
rs6457964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67854134	0.88[ASN][1000 genomes]
rs6901884	0.94[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6904504	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910832	0.84[YRI][hapmap]
rs6920322	0.85[ASN][1000 genomes]
rs6932038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932175	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934844	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];0.90[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757241	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7761425	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770155	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380616	0.85[YRI][hapmap]
rs9380618	0.85[YRI][hapmap]
rs9462238	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462239	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462240	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]
rs9470434	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470439	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9918461	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9969040	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997674	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9462241	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

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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