Variant report

Variant	rs2859365
Chromosome Location	chr6:28391465-28391466
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28390398..28392930-chr6:28395199..28398373,4	K562	blood:
2	chr6:28356707..28359445-chr6:28388134..28391982,4	K562	blood:
3	chr6:28389572..28392930-chr6:28395042..28397704,3	K562	blood:
4	chr6:28356866..28359445-chr6:28388346..28391982,3	K562	blood:
5	chr6:28370825..28372910-chr6:28390622..28392729,2	MCF-7	breast:
6	chr6:28385891..28388590-chr6:28390011..28392158,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN23-1	chr6:28390179-28391617	NONHSAT108462

No data

Extended variants
information (count: 43 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005125	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052215	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10946954	0.90[EUR][1000 genomes]
rs1124132	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1150705	0.81[EUR][1000 genomes]
rs1150707	0.92[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs1150709	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1150716	0.84[EUR][1000 genomes]
rs12214383	0.81[CEU][hapmap]
rs1233713	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13408	0.81[CEU][hapmap]
rs1361387	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1531681	0.81[CEU][hapmap]
rs1558205	0.81[TSI][hapmap]
rs1736895	0.81[CEU][hapmap]
rs2023493	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2108927	0.80[EUR][1000 genomes]
rs213228	0.80[MKK][hapmap]
rs213232	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs213236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs213237	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs213238	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs213240	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2142730	0.92[CEU][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs2247002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531803	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2531804	0.81[GIH][hapmap]
rs2531806	0.83[AMR][1000 genomes]
rs2531825	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2531831	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531832	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2859348	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs4455662	0.92[EUR][1000 genomes]
rs6899512	0.81[YRI][hapmap]
rs6912921	0.81[YRI][hapmap]
rs7206	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs728122	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853684	0.92[CEU][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs916403	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9301	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs9368565	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468372	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs2859365	AL022393.7	cis	Nerve Tibial	GTEx
rs2859365	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2859365	ZSCAN23	cis	parietal	SCAN
rs2859365	ZSCAN23	cis	Artery Tibial	GTEx
rs2859365	AL022393.7	cis	Muscle Skeletal	GTEx
rs2859365	AL022393.7	cis	lung	GTEx
rs2859365	ZSCAN23	cis	lymphoblastoid	seeQTL
rs2859365	ZNF323	cis	parietal	SCAN
rs2859365	ZNF323	cis	cerebellum	SCAN
rs2859365	ZSCAN23	cis	cerebellum	SCAN
rs2859365	ZKSCAN3	cis	parietal	SCAN
rs2859365	RP5-874C20.3	cis	Thyroid	GTEx
rs2859365	ZNF192	cis	cerebellum	SCAN
rs2859365	ZSCAN23	cis	Stomach	GTEx
rs2859365	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs2859365	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2859365	HIST1H2BL	cis	cerebellum	SCAN
rs2859365	ZSCAN31	cis	Muscle Skeletal	GTEx
rs2859365	ZSCAN31	cis	lung	GTEx
rs2859365	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs2859365	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs2859365	ZSCAN23	cis	lung	GTEx
rs2859365	AL022393.7	cis	Artery Tibial	GTEx
rs2859365	AL022393.7	cis	Esophagus Muscularis	GTEx
rs2859365	AL022393.7	cis	Artery Aorta	GTEx
rs2859365	ZSCAN31	cis	Thyroid	GTEx
rs2859365	ZNF96	cis	multi-tissue	Pritchard
rs2859365	ZNF323	cis	Frontal Cortex	GTEx
rs2859365	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs2859365	ZKSCAN3	cis	cerebellum	SCAN
rs2859365	ZNF323	cis	brain	seeQTL
rs2859365	ZSCAN23	cis	Muscle Skeletal	GTEx
rs2859365	ZNF187	cis	cerebellum	SCAN
rs2859365	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2859365	ZNF323	cis	multi-tissue	Pritchard

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
6	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:28385600-28410800	Weak transcription	Lung	lung
8	chr6:28385800-28391800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:28386000-28402200	Weak transcription	Osteobl	bone
10	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:28386600-28392200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:28386800-28392000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
17	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
21	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
23	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
25	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:28388400-28399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:28389000-28391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:28389000-28392600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:28389200-28393200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:28389200-28410200	Weak transcription	NHLF	lung
31	chr6:28389400-28393000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:28389400-28403200	Weak transcription	Adipose Nuclei	Adipose
33	chr6:28389400-28410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:28389600-28398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28389600-28409800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:28389600-28410200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:28389600-28410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:28389600-28410400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:28389800-28392000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:28389800-28392800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:28389800-28393000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:28389800-28410800	Weak transcription	Colonic Mucosa	Colon
43	chr6:28390000-28391600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:28390000-28391600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:28390000-28392400	Strong transcription	Fetal Brain Female	brain
46	chr6:28390000-28393200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:28390200-28391600	Strong transcription	NH-A	brain
48	chr6:28390200-28392600	Strong transcription	Fetal Lung	lung
49	chr6:28390200-28410400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:28390400-28392000	Strong transcription	HSMM	muscle

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