Variant report

Variant	rs2335408
Chromosome Location	chr1:154915977-154915978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154915676..154917776-chr1:155030028..155032426,2	MCF-7	breast:
2	chr1:154914807..154916848-chr1:155021073..155023957,2	MCF-7	breast:
3	chr1:154506433..154506946-chr1:154915914..154916857,2	MCF-7	breast:
4	chr1:154908783..154912738-chr1:154912911..154918149,9	K562	blood:
5	chr1:154910460..154912318-chr1:154915233..154917355,3	MCF-7	breast:
6	chr1:154641959..154642726-chr1:154915957..154916812,4	MCF-7	breast:
7	chr1:154641835..154642437-chr1:154915935..154916477,3	K562	blood:

Variant related genes	Relation type
ENSG00000270361	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1007170	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.97[ASN][1000 genomes]
rs10796934	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10796935	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908444	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10908445	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10908446	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908447	0.91[ASN][1000 genomes]
rs10908448	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109815	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264280	0.81[ASN][1000 genomes]
rs11264281	0.91[ASN][1000 genomes]
rs11264282	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264283	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264284	0.93[ASN][1000 genomes]
rs11264286	0.96[YRI][hapmap]
rs11264290	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264291	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12036859	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs12069356	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12095061	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130132	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1218582	0.81[CEU][hapmap];0.88[YRI][hapmap]
rs12406380	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1891805	0.96[YRI][hapmap]
rs1976559	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1977879	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2102423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135219	0.91[ASN][1000 genomes]
rs2174507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2211498	0.92[YRI][hapmap]
rs2335407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs2335409	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240874	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240875	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339857	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4578216	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4845398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845400	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845677	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4845678	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845679	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs4845680	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845681	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4845682	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845683	0.93[ASN][1000 genomes]
rs4845685	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845687	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845688	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845689	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845690	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845691	0.97[ASN][1000 genomes]
rs4845692	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4845693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845694	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845695	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4845696	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656435	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656494	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6669791	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6674853	0.97[ASN][1000 genomes]
rs6683557	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6686873	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689022	0.96[YRI][hapmap]
rs6699043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699080	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs705094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72702224	1.00[ASN][1000 genomes]
rs7528532	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7531728	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs7539805	0.95[YRI][hapmap]
rs7544528	0.83[ASN][1000 genomes]
rs7553195	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs869506	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs877343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883718	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs906593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9793588	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2335408	BCAN	cis	parietal	SCAN
rs2335408	CTSK	cis	parietal	SCAN
rs2335408	KCNN3	cis	parietal	SCAN
rs2335408	JTB	cis	parietal	SCAN
rs2335408	OAZ3	cis	parietal	SCAN
rs2335408	PBXIP1	cis	lymphoblastoid	seeQTL
rs2335408	KCNN3	cis	cerebellum	SCAN
rs2335408	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154910400-154916600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:154910400-154916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:154910400-154916800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:154910400-154917000	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:154910400-154920000	Weak transcription	Aorta	Aorta
6	chr1:154910400-154923000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:154910400-154925000	Weak transcription	Psoas Muscle	Psoas
8	chr1:154910600-154916800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:154910600-154927200	Weak transcription	Fetal Kidney	kidney
10	chr1:154910800-154916000	Weak transcription	HUVEC	blood vessel
11	chr1:154910800-154916200	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:154910800-154927200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:154910800-154927200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:154911000-154921400	Weak transcription	NHLF	lung
15	chr1:154911400-154916600	Weak transcription	Fetal Heart	heart
16	chr1:154911400-154917200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:154911800-154927400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:154911800-154927400	Weak transcription	NHEK	skin
19	chr1:154912200-154917600	Enhancers	Adipose Nuclei	Adipose
20	chr1:154912400-154917200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:154912600-154916000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:154912600-154916000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:154912600-154916600	Enhancers	Primary T cells from cord blood	blood
24	chr1:154912600-154916600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:154912600-154916600	Enhancers	Spleen	Spleen
26	chr1:154912600-154917000	Flanking Active TSS	GM12878-XiMat	blood
27	chr1:154912600-154917600	Enhancers	Brain Substantia Nigra	brain
28	chr1:154912600-154917800	Enhancers	Fetal Lung	lung
29	chr1:154912600-154917800	Enhancers	K562	blood
30	chr1:154912600-154919200	Genic enhancers	Fetal Muscle Leg	muscle
31	chr1:154912800-154917800	Enhancers	Stomach Mucosa	stomach
32	chr1:154913000-154916400	Weak transcription	Hela-S3	cervix
33	chr1:154913000-154920000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:154913000-154927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:154913200-154916800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:154913200-154927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:154913400-154917800	Enhancers	Fetal Intestine Large	intestine
38	chr1:154913400-154923000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:154913400-154925600	Weak transcription	Brain Germinal Matrix	brain
40	chr1:154913400-154927000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:154913600-154916200	Weak transcription	Small Intestine	intestine
42	chr1:154913600-154916800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:154913600-154916800	Enhancers	Brain Hippocampus Middle	brain
44	chr1:154913600-154918000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:154913800-154916800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:154913800-154916800	Genic enhancers	Thymus	Thymus
47	chr1:154913800-154917800	Enhancers	Placenta	Placenta
48	chr1:154913800-154918600	Enhancers	Liver	Liver
49	chr1:154914000-154916200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:154914000-154916400	Enhancers	Skeletal Muscle Male	skeletal muscle

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