Variant report

Variant	rs2934857
Chromosome Location	chr1:46039612-46039613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
2	chr1:45972767..45974304-chr1:46039504..46041198,2	K562	blood:
3	chr1:46031645..46033631-chr1:46038341..46040543,2	MCF-7	breast:
4	chr1:45985335..45987528-chr1:46038480..46041554,5	K562	blood:
5	chr1:45965940..45967492-chr1:46038830..46041668,2	K562	blood:
6	chr1:45973063..45975262-chr1:46038700..46040345,2	MCF-7	breast:
7	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
8	chr1:46023197..46024863-chr1:46038353..46040089,2	K562	blood:
9	chr1:46039552..46042482-chr1:46044610..46047405,2	K562	blood:
10	chr1:45965074..45967492-chr1:46039494..46041668,2	K562	blood:
11	chr1:46037943..46043170-chr1:46048057..46052696,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132763	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10430105	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs10430123	0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs10430124	0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs10749856	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs10789465	0.80[CHD][hapmap]
rs10789467	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10789470	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs10789471	0.92[CHD][hapmap]
rs1084086	0.90[CHD][hapmap]
rs10890333	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs10890334	0.82[CHB][hapmap]
rs10890335	0.83[CHB][hapmap]
rs10890336	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs10890341	0.83[CHB][hapmap]
rs10890346	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs11211129	0.85[CHD][hapmap]
rs11211142	0.97[ASN][1000 genomes]
rs11211145	0.92[CHD][hapmap]
rs11211147	0.80[CHB][hapmap]
rs11211149	0.81[CHB][hapmap]
rs11211152	0.92[CHD][hapmap]
rs11211157	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs11211161	0.97[CHD][hapmap]
rs11211163	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs11211166	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11211168	0.92[CHD][hapmap]
rs11211169	0.97[CHD][hapmap]
rs11211171	0.92[CHD][hapmap]
rs11211173	0.92[CHD][hapmap]
rs11211177	0.92[CHD][hapmap]
rs11211178	0.82[CHB][hapmap]
rs11211181	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs1135812	0.83[CHB][hapmap]
rs12024590	0.92[CHD][hapmap]
rs12037459	0.89[CHB][hapmap]
rs12043945	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12049027	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs12091503	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1250	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs12727696	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12743512	0.80[CHD][hapmap]
rs1547924	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs1547925	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs1972410	0.92[CHD][hapmap]
rs2050376	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs2088102	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2152078	0.92[CHD][hapmap]
rs2230657	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2230658	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs2230659	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2253862	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs2275085	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs2275086	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs2275276	0.80[CHD][hapmap]
rs28370457	0.92[CHD][hapmap]
rs28375469	0.97[CHD][hapmap]
rs28550303	0.97[CHD][hapmap]
rs28647556	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs28719889	0.92[CHD][hapmap]
rs28817701	0.81[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs28890893	0.92[CHD][hapmap]
rs2934858	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934859	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs2991972	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs2991973	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2991974	0.80[ASN][1000 genomes]
rs2991975	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2991976	0.96[ASN][1000 genomes]
rs2991977	0.85[ASN][1000 genomes]
rs2991979	0.92[CHD][hapmap]
rs2991981	0.85[ASN][1000 genomes]
rs2991985	0.81[ASN][1000 genomes]
rs2991986	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs2991987	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2991988	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs2991989	0.82[CHB][hapmap]
rs2993262	0.80[ASN][1000 genomes]
rs2993263	0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[ASN][1000 genomes]
rs3013595	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs3013597	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs3014210	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3014212	0.85[ASN][1000 genomes]
rs3014216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3014218	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014219	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3014220	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3014235	0.83[CHB][hapmap]
rs3014237	0.92[CHD][hapmap]
rs3014238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs3014239	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs3014241	0.92[CHD][hapmap]
rs3014242	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs3014245	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs3811436	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs4274104	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs4391704	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs4431884	0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs4439382	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs4468203	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4559551	0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs4564187	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs4607935	0.86[CHB][hapmap]
rs4609469	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs4660312	0.84[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4660313	0.92[CHD][hapmap]
rs4660876	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4660880	0.92[CHD][hapmap]
rs4660882	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4660883	0.82[CHB][hapmap];0.97[CHD][hapmap]
rs5021934	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs512083	0.89[EUR][1000 genomes]
rs518216	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs518365	0.85[CHD][hapmap]
rs523526	0.80[ASN][1000 genomes]
rs563799	0.92[ASN][1000 genomes]
rs592214	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs606542	0.80[ASN][1000 genomes]
rs622798	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs6429576	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs659437	0.97[ASN][1000 genomes]
rs6656279	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6658700	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs667626	0.80[ASN][1000 genomes]
rs6694889	0.82[CHB][hapmap]
rs6697821	0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs937291	0.80[CHD][hapmap]
rs9429085	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs2934857	GPBP1L1	cis	Whole Blood	GTEx
rs2934857	MAST2	cis	Artery Tibial	GTEx
rs2934857	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2934857	CCDC163P	cis	Stomach	GTEx
rs2934857	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2934857	CCDC163P	cis	Thyroid	GTEx
rs2934857	TESK2	cis	cerebellum	SCAN
rs2934857	AKR1A1	cis	cerebellum	SCAN
rs2934857	CCDC163P	cis	lung	GTEx
rs2934857	CCDC163P	cis	Artery Aorta	GTEx
rs2934857	CCDC163P	cis	Muscle Skeletal	GTEx
rs2934857	CCDC163P	cis	Nerve Tibial	GTEx
rs2934857	CYP4Z2P	cis	cerebellum	SCAN
rs2934857	ATPAF1	cis	cerebellum	SCAN
rs2934857	NSUN4	cis	cerebellum	SCAN
rs2934857	C1orf84	cis	cerebellum	SCAN
rs2934857	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2934857	MAST2	cis	Artery Aorta	GTEx
rs2934857	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs2934857	CCDC163P	cis	Whole Blood	GTEx
rs2934857	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2934857	CCDC163P	cis	Artery Tibial	GTEx
rs2934857	CYP4Z2P	cis	parietal	SCAN
rs2934857	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2934857	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2934857	IPP	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46032600-46049000	Weak transcription	Right Atrium	heart
2	chr1:46033000-46048800	Weak transcription	Fetal Brain Male	brain
3	chr1:46034200-46039800	Weak transcription	Small Intestine	intestine
4	chr1:46034200-46048800	Weak transcription	Stomach Mucosa	stomach
5	chr1:46035000-46041000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:46035000-46042600	Weak transcription	HMEC	breast
7	chr1:46035400-46048800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:46035600-46048000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:46035600-46048800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:46035800-46039800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:46035800-46040000	Weak transcription	Left Ventricle	heart
12	chr1:46035800-46041000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:46035800-46041800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:46035800-46048800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:46035800-46048800	Weak transcription	Hela-S3	cervix
16	chr1:46036200-46047600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:46036200-46048800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:46036400-46039800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:46036400-46039800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:46036400-46039800	Weak transcription	Fetal Stomach	stomach
21	chr1:46036400-46041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:46036400-46048000	Weak transcription	Spleen	Spleen
23	chr1:46036400-46048600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:46036400-46048800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:46036400-46048800	Weak transcription	Brain Germinal Matrix	brain
26	chr1:46036400-46049200	Weak transcription	Gastric	stomach
27	chr1:46036600-46039800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:46036600-46039800	Weak transcription	HUVEC	blood vessel
29	chr1:46036600-46040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:46036600-46040200	Weak transcription	HSMMtube	muscle
31	chr1:46036600-46040200	Weak transcription	NHEK	skin
32	chr1:46036600-46047400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:46036600-46048200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:46036600-46048600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:46036600-46048600	Weak transcription	Lung	lung
36	chr1:46036600-46048800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:46036600-46048800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:46036600-46048800	Weak transcription	Fetal Kidney	kidney
39	chr1:46036600-46048800	Weak transcription	Fetal Lung	lung
40	chr1:46036600-46048800	Weak transcription	Dnd41	blood
41	chr1:46036600-46048800	Weak transcription	HepG2	liver
42	chr1:46036800-46039800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:46036800-46040200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:46036800-46040400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:46036800-46040600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:46036800-46040600	Weak transcription	HSMM	muscle
47	chr1:46036800-46040600	Weak transcription	NHDF-Ad	bronchial
48	chr1:46036800-46040600	Weak transcription	NHLF	lung
49	chr1:46036800-46041600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:46036800-46042000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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