Variant report

Variant	rs2765229
Chromosome Location	chr6:28892919-28892920
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28886841-28892929	HepG2	liver:	n/a	n/a
2	IRF1	chr6:28892873-28893139	K562	blood:	n/a	n/a
3	POLR2A	chr6:28889603-28892955	K562	blood:	n/a	n/a
4	POLR2A	chr6:28889311-28892929	GM12891	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28887886..28894013-chr6:28935014..28940220,8	K562	blood:
2	chr6:28890449..28893259-chr6:28971754..28975345,6	K562	blood:
3	chr6:28890727..28894097-chr6:28943047..28947323,5	MCF-7	breast:
4	chr6:28831640..28835125-chr6:28890004..28893108,3	MCF-7	breast:
5	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
6	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
7	chr6:28892042..28894995-chr6:28981382..28984107,2	K562	blood:
8	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
9	chr6:27856359..27859269-chr6:28891133..28894008,2	MCF-7	breast:
10	chr6:28891456..28893478-chr6:28954362..28956726,2	K562	blood:
11	chr6:28890160..28893119-chr6:28970726..28976038,6	K562	blood:
12	chr6:28831633..28833233-chr6:28890419..28893119,2	K562	blood:
13	chr6:28804831..28806391-chr6:28892543..28895335,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM27	TF binding region
ENSG00000263426	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000228666	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000197935	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1002925	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1005123	0.83[ASN][1000 genomes]
rs1237485	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476016	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543796	0.82[ASN][1000 genomes]
rs169683	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1794587	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs184093	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2006173	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2013848	0.89[ASN][1000 genomes]
rs2032500	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071785	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2071790	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209122	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs209126	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209128	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209129	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209137	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209138	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209148	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209149	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs209152	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs209153	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209160	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209161	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209163	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209164	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209169	0.81[EUR][1000 genomes]
rs209171	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209173	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209175	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs209176	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209179	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209184	0.87[EUR][1000 genomes]
rs209186	0.86[EUR][1000 genomes]
rs2157312	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2157313	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2179648	0.80[ASN][1000 genomes]
rs2187807	0.91[ASN][1000 genomes]
rs2187808	0.91[ASN][1000 genomes]
rs2208536	0.86[EUR][1000 genomes]
rs2269555	0.84[ASN][1000 genomes]
rs2394512	0.82[ASN][1000 genomes]
rs2754764	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754767	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2765218	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2765219	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129792	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3129793	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130841	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130842	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130843	0.81[AFR][1000 genomes]
rs3130886	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130889	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130897	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131070	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3131074	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131077	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131100	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131102	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131342	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3132371	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3132386	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3135303	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135315	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3135319	0.81[EUR][1000 genomes]
rs3135321	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135322	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3135323	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135324	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135326	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3135327	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3135328	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs377392	0.87[EUR][1000 genomes]
rs381808	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs386628	0.87[EUR][1000 genomes]
rs393431	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4427026	0.89[ASN][1000 genomes]
rs4713186	0.89[ASN][1000 genomes]
rs4713187	0.88[ASN][1000 genomes]
rs4713188	0.89[ASN][1000 genomes]
rs4713190	0.86[ASN][1000 genomes]
rs4713192	0.86[ASN][1000 genomes]
rs4947339	0.89[ASN][1000 genomes]
rs526983	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456876	0.91[ASN][1000 genomes]
rs6456880	0.85[ASN][1000 genomes]
rs6456883	0.84[ASN][1000 genomes]
rs6901599	0.91[ASN][1000 genomes]
rs6904975	0.84[ASN][1000 genomes]
rs6906909	0.84[ASN][1000 genomes]
rs6914955	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6916161	0.84[ASN][1000 genomes]
rs6920392	0.86[ASN][1000 genomes]
rs6931823	0.89[ASN][1000 genomes]
rs763009	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7743189	0.87[ASN][1000 genomes]
rs7755875	0.87[ASN][1000 genomes]
rs7761547	0.89[ASN][1000 genomes]
rs7768299	0.82[ASN][1000 genomes]
rs9257229	0.80[EUR][1000 genomes]
rs9257401	0.89[ASN][1000 genomes]
rs9257404	0.87[ASN][1000 genomes]
rs9257405	0.89[ASN][1000 genomes]
rs9257408	0.82[ASN][1000 genomes]
rs9257421	0.89[ASN][1000 genomes]
rs9257447	0.85[ASN][1000 genomes]
rs9257449	0.85[ASN][1000 genomes]
rs9257455	0.82[ASN][1000 genomes]
rs9257461	0.84[ASN][1000 genomes]
rs9348816	0.82[ASN][1000 genomes]
rs9393939	0.82[ASN][1000 genomes]
rs9468467	0.80[ASN][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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2765229	ZNF323	cis	parietal	SCAN
rs2765229	ZSCAN16	cis	parietal	SCAN
rs2765229	ZSCAN23	cis	cerebellum	SCAN
rs2765229	NKAPL	cis	parietal	SCAN
rs2765229	HIST1H2BH	cis	cerebellum	SCAN
rs2765229	ZSCAN23	cis	parietal	SCAN
rs2765229	RFP	cis	multi-tissue	Pritchard
rs2765229	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28890200-28893000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28892000-28893000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:28892200-28893000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:28892200-28893000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr6:28892200-28893400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:28892400-28893000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:28892400-28893000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:28892400-28893000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:28892400-28893000	Flanking Active TSS	Dnd41	blood
10	chr6:28892400-28893000	Flanking Active TSS	HepG2	liver
11	chr6:28892400-28893400	Flanking Active TSS	K562	blood
12	chr6:28892600-28893000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr6:28892600-28893000	Enhancers	Brain Hippocampus Middle	brain
14	chr6:28892600-28893000	Enhancers	Fetal Brain Female	brain
15	chr6:28892600-28893000	Enhancers	HUVEC	blood vessel
16	chr6:28892600-28895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:28892600-28895800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:28892800-28893000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:28892800-28893000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:28892800-28893000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:28892800-28893000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr6:28892800-28893000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:28892800-28893000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:28892800-28893000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:28892800-28893000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:28892800-28893000	Enhancers	GM12878-XiMat	blood
27	chr6:28892800-28893000	Enhancers	Hela-S3	cervix
28	chr6:28892800-28895200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:28892800-28895400	Weak transcription	Primary B cells from cord blood	blood
30	chr6:28892800-28895400	Weak transcription	Fetal Kidney	kidney
31	chr6:28892800-28895600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:28892800-28895800	Weak transcription	Fetal Intestine Small	intestine
33	chr6:28892800-28896000	Weak transcription	Fetal Intestine Large	intestine
34	chr6:28892800-28897600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:28892800-28897600	Weak transcription	Monocytes-CD14+_RO01746	blood

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