Variant report

Variant	rs1378125
Chromosome Location	chr8:98938413-98938414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:98933138..98936017-chr8:98937438..98939186,2	MCF-7	breast:
2	chr8:98933283..98934888-chr8:98936551..98939414,2	K562	blood:
3	chr8:98938075..98940627-chr8:98940797..98943722,2	K562	blood:
4	chr8:98936307..98939164-chr8:98941664..98943484,3	K562	blood:

Variant related genes	Relation type
ENSG00000132561	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10091886	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1020654	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1020655	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11996155	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12548243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550816	0.88[ASW][hapmap];0.84[LWK][hapmap];0.80[TSI][hapmap]
rs1378123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840370	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1840371	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1840372	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968721	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256367	0.82[CEU][hapmap]
rs2444879	0.89[JPT][hapmap]
rs2444899	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2444900	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2444902	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2444903	0.82[CEU][hapmap]
rs2512034	0.86[JPT][hapmap]
rs2512035	0.89[JPT][hapmap]
rs2512072	0.95[CEU][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2513835	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2513836	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2513837	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[EUR][1000 genomes]
rs2513838	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2513839	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2513845	0.89[JPT][hapmap]
rs2513846	0.89[JPT][hapmap]
rs2513847	0.88[JPT][hapmap]
rs2513851	1.00[JPT][hapmap]
rs2959646	0.91[CEU][hapmap]
rs4298468	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4512352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6468603	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897190	0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1028055	chr8:98780445-98977746	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active 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	26 gene(s)	inside rSNPs	diseases
4	nsv891214	chr8:98849303-98990399	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv891215	chr8:98910287-98980663	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1378125	NCALD	cis	parietal	SCAN
rs1378125	PGCP	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98929200-98944800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:98930800-98950000	Weak transcription	Right Ventricle	heart
3	chr8:98931000-98938600	Weak transcription	Placenta	Placenta
4	chr8:98931000-98940800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:98931200-98944200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:98931800-98943200	Enhancers	Fetal Muscle Leg	muscle
7	chr8:98932000-98940800	Weak transcription	Ovary	ovary
8	chr8:98932200-98943400	Weak transcription	Pancreas	Pancrea
9	chr8:98932400-98940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:98934200-98943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr8:98934800-98938800	Enhancers	Adipose Nuclei	Adipose
12	chr8:98935200-98941200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:98935200-98941200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr8:98935200-98944400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:98935400-98941200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr8:98935400-98941200	Weak transcription	Brain Anterior Caudate	brain
17	chr8:98935800-98941000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:98936800-98938800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr8:98937000-98939000	Enhancers	Stomach Mucosa	stomach
20	chr8:98937000-98940800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr8:98937200-98938800	Enhancers	Fetal Lung	lung
22	chr8:98937200-98939000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr8:98937200-98939400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:98937400-98939200	Enhancers	Liver	Liver
25	chr8:98937600-98938600	Enhancers	Fetal Heart	heart
26	chr8:98937600-98939000	Enhancers	Fetal Stomach	stomach
27	chr8:98937600-98939400	Enhancers	NHDF-Ad	bronchial
28	chr8:98937800-98938600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr8:98937800-98938800	Enhancers	Brain Hippocampus Middle	brain
30	chr8:98937800-98938800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:98937800-98938800	Enhancers	NHLF	lung
32	chr8:98937800-98938800	Enhancers	Osteobl	bone
33	chr8:98937800-98939000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:98937800-98939000	Enhancers	Fetal Intestine Small	intestine
35	chr8:98937800-98939200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:98937800-98939200	Enhancers	Fetal Intestine Large	intestine
37	chr8:98937800-98939400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr8:98938000-98938600	Enhancers	Brain Substantia Nigra	brain
39	chr8:98938000-98938600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr8:98938000-98938600	Enhancers	NH-A	brain
41	chr8:98938000-98938800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:98938000-98938800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:98938000-98939200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:98938200-98938600	Enhancers	H9 Cell Line	embryonic stem cell
45	chr8:98938200-98938600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr8:98938200-98938600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:98938200-98938600	Enhancers	Brain Angular Gyrus	brain
48	chr8:98938200-98938600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr8:98938200-98938600	Enhancers	HUVEC	blood vessel
50	chr8:98938200-98939000	Enhancers	Right Atrium	heart

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