Variant report

Variant	rs4896852
Chromosome Location	chr6:146284621-146284622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146054881..146058754-chr6:146284576..146286666,3	K562	blood:
2	chr6:146247179..146250134-chr6:146283197..146284955,2	K562	blood:
3	chr6:146133534..146136752-chr6:146283932..146287911,4	K562	blood:
4	chr6:146133507..146136027-chr6:146282188..146284857,3	K562	blood:
5	chr6:146275961..146278113-chr6:146283036..146285650,2	MCF-7	breast:
6	chr6:146051601..146058492-chr6:146282422..146286666,8	K562	blood:

Variant related genes	Relation type
ENSG00000270828	Chromatin interaction
ENSG00000235652	Chromatin interaction
ENSG00000146414	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000118496	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10223508	0.98[EUR][1000 genomes]
rs10457792	0.82[EUR][1000 genomes]
rs10457793	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10457794	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10457795	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1062067	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1062068	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10872582	0.86[EUR][1000 genomes]
rs10872583	0.84[EUR][1000 genomes]
rs11155452	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1133832	0.92[EUR][1000 genomes]
rs11755334	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11760	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12194437	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13198450	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13204280	0.81[EUR][1000 genomes]
rs1331636	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331637	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331639	0.81[EUR][1000 genomes]
rs1331645	0.84[EUR][1000 genomes]
rs1412081	0.82[EUR][1000 genomes]
rs1474871	0.83[EUR][1000 genomes]
rs1986729	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2073287	0.87[EUR][1000 genomes]
rs2144477	0.83[EUR][1000 genomes]
rs2144478	0.86[EUR][1000 genomes]
rs2207785	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2224120	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2224121	0.90[EUR][1000 genomes]
rs2243665	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2246334	0.82[ASN][1000 genomes]
rs2247206	0.93[EUR][1000 genomes]
rs2247211	0.93[EUR][1000 genomes]
rs2247317	0.84[EUR][1000 genomes]
rs2247429	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247666	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249386	0.82[ASN][1000 genomes]
rs2250387	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2253194	0.82[EUR][1000 genomes]
rs2253307	0.82[EUR][1000 genomes]
rs2253654	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253764	0.82[EUR][1000 genomes]
rs2253768	0.83[EUR][1000 genomes]
rs2253880	0.82[EUR][1000 genomes]
rs2253886	0.82[EUR][1000 genomes]
rs2253887	0.80[EUR][1000 genomes]
rs2254257	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2254283	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2254288	0.92[EUR][1000 genomes]
rs2256998	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2265467	0.84[EUR][1000 genomes]
rs2265468	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265469	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265471	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265472	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265474	0.82[ASN][1000 genomes]
rs2265477	0.84[EUR][1000 genomes]
rs2265915	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265917	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265918	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265919	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2328712	0.90[EUR][1000 genomes]
rs2474356	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2485632	0.80[EUR][1000 genomes]
rs2492855	0.90[EUR][1000 genomes]
rs2748482	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2748483	0.90[EUR][1000 genomes]
rs2748484	0.90[EUR][1000 genomes]
rs2748485	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2748486	0.84[EUR][1000 genomes]
rs2748487	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2748499	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2748500	0.82[EUR][1000 genomes]
rs2748502	0.91[EUR][1000 genomes]
rs2777476	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2777477	0.91[EUR][1000 genomes]
rs2777484	0.89[EUR][1000 genomes]
rs2814866	0.90[EUR][1000 genomes]
rs2814867	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814869	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2814874	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814875	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814876	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814877	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814879	0.82[EUR][1000 genomes]
rs2814880	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2892453	0.86[EUR][1000 genomes]
rs3923579	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924498	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924499	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924502	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4075694	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4075695	0.89[EUR][1000 genomes]
rs4075696	0.89[EUR][1000 genomes]
rs4243478	0.90[EUR][1000 genomes]
rs4280983	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314514	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4316025	0.87[EUR][1000 genomes]
rs4360151	0.98[EUR][1000 genomes]
rs4391282	0.99[EUR][1000 genomes]
rs4435956	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4566902	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56181683	0.92[EUR][1000 genomes]
rs62435810	0.81[ASN][1000 genomes]
rs6570736	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6570738	0.81[EUR][1000 genomes]
rs6908063	0.83[EUR][1000 genomes]
rs6910790	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6913797	0.81[EUR][1000 genomes]
rs6914813	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6917482	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6922507	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923545	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6924159	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926076	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6926657	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6930975	0.86[EUR][1000 genomes]
rs6934467	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6938972	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7739418	0.87[EUR][1000 genomes]
rs7747576	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7753092	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7753696	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755440	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854145	0.87[EUR][1000 genomes]
rs864390	0.91[EUR][1000 genomes]
rs866473	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322043	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322046	0.85[EUR][1000 genomes]
rs9322047	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9322048	0.83[EUR][1000 genomes]
rs932522	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373485	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9376970	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376971	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9376975	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386141	0.99[EUR][1000 genomes]
rs9390365	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390377	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9399569	0.96[EUR][1000 genomes]
rs9399571	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9399573	0.82[EUR][1000 genomes]
rs9403755	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9403756	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9403757	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9403764	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403765	0.86[EUR][1000 genomes]
rs9403767	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9403768	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9497424	0.94[EUR][1000 genomes]
rs9497425	0.96[EUR][1000 genomes]
rs9497427	0.97[EUR][1000 genomes]
rs9497431	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9497434	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9497435	0.99[EUR][1000 genomes]
rs969694	0.84[EUR][1000 genomes]
rs9791313	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4896852	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146282400-146284800	Weak transcription	Spleen	Spleen
2	chr6:146282600-146286400	Active TSS	GM12878-XiMat	blood
3	chr6:146282800-146284800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:146283000-146286400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:146283400-146284800	Flanking Active TSS	Liver	Liver
6	chr6:146283400-146286200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:146283600-146286000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:146283600-146286000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:146283600-146286000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:146283600-146286000	Active TSS	K562	blood
11	chr6:146283600-146286200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:146283600-146286200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:146283600-146286400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:146283800-146284800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:146283800-146285400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:146283800-146286200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:146283800-146286200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:146283800-146286200	Active TSS	Aorta	Aorta
19	chr6:146283800-146286400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:146283800-146286400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:146283800-146286400	Active TSS	Psoas Muscle	Psoas
22	chr6:146284000-146284800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr6:146284000-146284800	Flanking Active TSS	HUVEC	blood vessel
24	chr6:146284000-146285000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr6:146284000-146285200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:146284000-146285800	Active TSS	Fetal Muscle Leg	muscle
27	chr6:146284000-146286000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:146284000-146286000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:146284000-146286000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr6:146284000-146286200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:146284000-146286200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:146284000-146286200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:146284000-146286200	Active TSS	Right Atrium	heart
34	chr6:146284000-146286200	Active TSS	Stomach Smooth Muscle	stomach
35	chr6:146284000-146286200	Active TSS	A549	lung
36	chr6:146284000-146286200	Active TSS	Hela-S3	cervix
37	chr6:146284000-146286200	Active TSS	NHDF-Ad	bronchial
38	chr6:146284000-146286200	Active TSS	NHLF	lung
39	chr6:146284000-146286400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:146284000-146286400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:146284000-146286400	Active TSS	HMEC	breast
42	chr6:146284200-146284800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr6:146284200-146284800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr6:146284200-146284800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:146284200-146284800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr6:146284200-146285200	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr6:146284200-146285400	Bivalent/Poised TSS	HepG2	liver
48	chr6:146284200-146286000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:146284200-146286000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr6:146284200-146286000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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