Variant report

Variant	rs2934859
Chromosome Location	chr1:46017836-46017837
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45476252..45479466-chr1:46015891..46017851,3	K562	blood:
2	chr1:46014904..46019071-chr1:46034504..46037164,4	K562	blood:
3	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
4	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
5	chr1:45195042..45198446-chr1:46014587..46018125,4	K562	blood:
6	chr1:46015193..46018509-chr1:46048657..46051369,3	MCF-7	breast:
7	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
8	chr1:45993856..45997631-chr1:46016442..46019336,3	K562	blood:
9	chr1:46017262..46018085-chr11:64544823..64545724,2	Hela-S3	cervix:
10	chr1:45974303..45976315-chr1:46016860..46019727,2	K562	blood:
11	chr1:45974939..45977846-chr1:46015282..46017928,2	MCF-7	breast:
12	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
13	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
14	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
15	chr1:46016158..46018280-chr1:46030299..46033160,3	K562	blood:
16	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
17	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117448	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000234379	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000236624	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10430105	0.90[CHD][hapmap]
rs10749856	0.95[JPT][hapmap]
rs10789465	1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10789467	0.95[JPT][hapmap]
rs10789470	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs10789471	0.95[CHD][hapmap]
rs1084086	0.92[CHD][hapmap]
rs10890333	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs10890336	1.00[JPT][hapmap]
rs11211122	0.80[EUR][1000 genomes]
rs11211129	1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11211130	0.84[EUR][1000 genomes]
rs11211135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211136	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211145	0.95[CHD][hapmap]
rs11211152	0.95[CHD][hapmap]
rs11211157	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs11211161	0.90[CHD][hapmap]
rs11211163	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs11211166	1.00[JPT][hapmap]
rs11211168	0.95[CHD][hapmap]
rs11211169	0.90[CHD][hapmap]
rs11211171	0.95[CHD][hapmap]
rs11580609	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11582118	0.80[EUR][1000 genomes]
rs12024590	0.95[CHD][hapmap]
rs12043945	0.95[JPT][hapmap]
rs12049027	0.94[JPT][hapmap]
rs12091503	0.95[JPT][hapmap]
rs12133294	0.84[EUR][1000 genomes]
rs1250	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs12568144	0.81[EUR][1000 genomes]
rs12743512	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs1547924	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs1547925	0.90[CHD][hapmap]
rs1972410	0.95[CHD][hapmap]
rs2050376	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs2088102	0.81[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs2152078	0.95[CHD][hapmap]
rs2230657	0.90[JPT][hapmap]
rs2230658	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs2230659	0.95[JPT][hapmap]
rs2253862	0.90[CHD][hapmap]
rs2275085	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs2275086	0.90[CHD][hapmap]
rs2275276	1.00[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2356551	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356553	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2453404	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28370457	0.95[CHD][hapmap]
rs28375469	0.90[CHD][hapmap]
rs28550303	0.90[CHD][hapmap]
rs28647556	0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs28719889	0.95[CHD][hapmap]
rs28817701	0.92[CHD][hapmap];0.90[JPT][hapmap]
rs28890893	0.95[CHD][hapmap]
rs2934856	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2934857	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs2934858	0.80[ASN][1000 genomes]
rs2991970	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2991971	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2991972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991973	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2991974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991975	0.81[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs2991979	0.95[CHD][hapmap]
rs2991986	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs2991987	0.95[JPT][hapmap]
rs2991988	0.90[CHD][hapmap]
rs2993262	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993263	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3013595	0.81[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs3013597	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs3014210	0.92[CHD][hapmap];0.84[JPT][hapmap]
rs3014216	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3014218	0.91[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs3014219	0.93[ASN][1000 genomes]
rs3014220	0.98[ASN][1000 genomes]
rs3014237	0.95[CHD][hapmap]
rs3014238	0.82[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs3014239	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs3014241	0.95[CHD][hapmap]
rs3014242	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs3014245	0.90[CHD][hapmap]
rs35092140	0.82[EUR][1000 genomes]
rs3811436	0.90[CHD][hapmap]
rs4431884	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs4439382	0.90[CHD][hapmap]
rs4468203	0.94[JPT][hapmap]
rs4559551	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs4564187	0.95[JPT][hapmap]
rs4609469	0.95[JPT][hapmap]
rs4660312	0.95[CHD][hapmap];0.89[JPT][hapmap]
rs4660313	0.95[CHD][hapmap]
rs4660869	0.83[EUR][1000 genomes]
rs4660876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660880	0.95[CHD][hapmap]
rs4660882	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs5021934	0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs512026	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs518216	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs518365	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs523526	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592214	0.98[ASN][1000 genomes]
rs60608374	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs606542	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622798	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429576	0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs644915	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656279	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6658700	0.90[CHD][hapmap]
rs6661321	0.80[EUR][1000 genomes]
rs666720	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs667626	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697821	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs7526571	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7526665	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7903	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937291	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs9429079	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429085	0.89[ASN][1000 genomes]
rs945180	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2934859	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2934859	CYP4Z2P	cis	cerebellum	SCAN
rs2934859	CCDC163P	cis	Nerve Tibial	GTEx
rs2934859	CYP4Z2P	cis	parietal	SCAN
rs2934859	CCDC163P	cis	Muscle Skeletal	GTEx
rs2934859	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs2934859	CCDC163P	cis	Stomach	GTEx
rs2934859	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2934859	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs2934859	TESK2	cis	cerebellum	SCAN
rs2934859	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2934859	IPP	cis	lymphoblastoid	seeQTL
rs2934859	CCDC163P	cis	Artery Tibial	GTEx
rs2934859	CCDC163P	cis	Whole Blood	GTEx
rs2934859	GPBP1L1	cis	Whole Blood	GTEx
rs2934859	CCDC163P	cis	Thyroid	GTEx
rs2934859	CCDC163P	cis	lung	GTEx
rs2934859	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2934859	C1orf84	cis	cerebellum	SCAN
rs2934859	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2934859	MAST2	cis	Artery Tibial	GTEx
rs2934859	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46016000-46018000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:46016000-46018000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:46016000-46018000	Active TSS	Pancreas	Pancrea
4	chr1:46016000-46018200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:46016000-46018200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:46016800-46018200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:46016800-46018400	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr1:46016800-46018400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:46017000-46018000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:46017000-46018000	Flanking Active TSS	Fetal Brain Female	brain
11	chr1:46017000-46018000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr1:46017000-46018000	Flanking Active TSS	Dnd41	blood
13	chr1:46017000-46018200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:46017000-46018200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:46017000-46018400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:46017000-46018600	Flanking Active TSS	Liver	Liver
17	chr1:46017000-46025800	Weak transcription	Spleen	Spleen
18	chr1:46017200-46018000	Flanking Active TSS	Fetal Muscle Leg	muscle
19	chr1:46017200-46018000	Active TSS	HepG2	liver
20	chr1:46017200-46018200	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr1:46017200-46018400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:46017200-46018400	Flanking Active TSS	NHEK	skin
23	chr1:46017200-46018600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr1:46017400-46018000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:46017400-46018000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:46017400-46018000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:46017400-46018000	Transcr. at gene 5' and 3'	Stomach Mucosa	stomach
28	chr1:46017400-46018000	Flanking Active TSS	HMEC	breast
29	chr1:46017400-46018000	Flanking Active TSS	NH-A	brain
30	chr1:46017400-46018200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:46017400-46018200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:46017400-46018200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:46017400-46018200	Flanking Active TSS	GM12878-XiMat	blood
34	chr1:46017400-46018400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:46017400-46018400	Flanking Active TSS	Hela-S3	cervix
36	chr1:46017400-46020000	Weak transcription	Ovary	ovary
37	chr1:46017400-46023000	Weak transcription	Psoas Muscle	Psoas
38	chr1:46017400-46027000	Weak transcription	Aorta	Aorta
39	chr1:46017400-46027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:46017600-46018000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:46017600-46018000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:46017600-46018000	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr1:46017600-46018000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:46017600-46018000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:46017600-46018000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:46017600-46018200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:46017600-46018200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
48	chr1:46017600-46018200	Enhancers	Primary T cells from cord blood	blood
49	chr1:46017600-46018200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr1:46017600-46018200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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