Variant report

Variant	rs1015690
Chromosome Location	chr6:28390526-28390527
allele	G/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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 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	chr6:28385891..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: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10484540	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484541	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1555046	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1555047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1556957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16894121	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17313059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17313276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17314224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17314865	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17314991	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17315340	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17315648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17315739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17316033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17392982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17393066	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17393342	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17393506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17393786	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393918	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17720687	0.82[CEU][hapmap]
rs2027362	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2072318	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs213230	0.88[CHB][hapmap]
rs213231	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs2232419	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2232434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2232438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734562	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56001748	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56787378	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57126418	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57204212	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57366176	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59732975	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60184496	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60660967	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915122	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740609	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73740620	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740622	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740623	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742547	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742550	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742551	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742555	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73742558	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs758396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468378	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9717944	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1015690	ZNF96	cis	multi-tissue	Pritchard
rs1015690	ZSCAN12	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 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	chr6:28380800-28390600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:28383400-28390600	Weak transcription	Fetal Stomach	stomach
4	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
5	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:28384800-28390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:28385000-28390600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:28385200-28390600	Weak transcription	Placenta	Placenta
10	chr6:28385400-28391000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:28385400-28391200	Weak transcription	HSMMtube	muscle
12	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
13	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:28385600-28390800	Weak transcription	Aorta	Aorta
15	chr6:28385600-28390800	Weak transcription	Ovary	ovary
16	chr6:28385600-28410800	Weak transcription	Lung	lung
17	chr6:28385800-28390800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:28385800-28391800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:28386000-28402200	Weak transcription	Osteobl	bone
20	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:28386200-28390600	Weak transcription	Right Ventricle	heart
22	chr6:28386200-28391000	Weak transcription	Psoas Muscle	Psoas
23	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:28386600-28391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:28386600-28392200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:28386800-28392000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
30	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:28387400-28390600	Weak transcription	Fetal Intestine Large	intestine
32	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:28387800-28390600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:28387800-28390600	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:28387800-28390800	Weak transcription	Brain Anterior Caudate	brain
37	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
38	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
40	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
42	chr6:28388400-28390600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:28388400-28399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:28388800-28390800	Weak transcription	Left Ventricle	heart
46	chr6:28389000-28391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:28389000-28391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:28389000-28392600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:28389200-28390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:28389200-28393200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links