Variant report

Variant	rs1045827
Chromosome Location	chr1:120162442-120162443
allele	C/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	chr1:120161780..120163387-chr1:120165272..120166902,2	MCF-7	breast:
2	chr1:120160558..120163551-chr1:120189552..120191710,2	MCF-7	breast:
3	chr1:120161786..120164966-chr1:120184691..120189749,4	K562	blood:
4	chr1:120162086..120165079-chr1:120173514..120175556,2	MCF-7	breast:
5	chr1:120161786..120164966-chr1:120187188..120189749,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF697-2	chr1:120162038-120164121	NONHSAT005572

No data

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10754415	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10754416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802120	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10802123	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802126	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10923878	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10923879	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024934	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12064265	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12067843	0.94[ASN][1000 genomes]
rs12076924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079724	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281493	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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795662	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795663	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850870	0.99[ASN][1000 genomes]
rs3862260	0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3862261	0.99[ASN][1000 genomes]
rs3862262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4079793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4659218	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4659219	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4659221	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656016	0.84[JPT][hapmap]
rs699775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552885	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];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2756860	chr1:120098661-120162442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv463317	chr1:120107602-120162787	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv547618	chr1:120107602-120162787	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv872179	chr1:120131597-120162787	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1045827	HSD3B2	cis	cerebellum	SCAN
rs1045827	NBPF7	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120146200-120165000	Weak transcription	Aorta	Aorta
2	chr1:120152200-120167800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:120153200-120164400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:120154400-120163400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:120154400-120167400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:120154600-120163400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:120154600-120164200	Weak transcription	Fetal Intestine Large	intestine
8	chr1:120154600-120165000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:120154600-120165000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:120154600-120165000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:120154800-120164200	Weak transcription	Liver	Liver
12	chr1:120154800-120164600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:120154800-120164800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:120154800-120165000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:120154800-120165200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:120154800-120165400	Weak transcription	Fetal Brain Male	brain
17	chr1:120154800-120173600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:120155200-120164200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:120156800-120163000	Weak transcription	HUVEC	blood vessel
20	chr1:120156800-120163600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:120156800-120164600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:120156800-120165400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:120156800-120169800	Weak transcription	NHDF-Ad	bronchial
24	chr1:120156800-120173800	Weak transcription	Colonic Mucosa	Colon
25	chr1:120157000-120164800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:120157200-120165000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:120157200-120165200	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:120157200-120165400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:120157400-120167800	Weak transcription	Fetal Kidney	kidney
30	chr1:120158400-120169800	Weak transcription	NH-A	brain
31	chr1:120158800-120162600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:120159200-120163000	Enhancers	Fetal Heart	heart
33	chr1:120159800-120164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:120159800-120165000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:120159800-120165200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:120159800-120165400	Weak transcription	GM12878-XiMat	blood
37	chr1:120159800-120166600	Weak transcription	K562	blood
38	chr1:120160800-120163600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:120161000-120164600	Weak transcription	Brain Germinal Matrix	brain
40	chr1:120161000-120165200	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:120161000-120170200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:120161200-120163600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:120161200-120164000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:120161200-120164000	Weak transcription	NHEK	skin
45	chr1:120161200-120165200	Weak transcription	Gastric	stomach
46	chr1:120161200-120165200	Weak transcription	Right Ventricle	heart
47	chr1:120161200-120165400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:120161200-120165400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:120161200-120168600	Strong transcription	Placenta	Placenta
50	chr1:120161400-120163600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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