Variant report

Variant	rs12030275
Chromosome Location	chr1:70877743-70877744
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70876951..70877911-chr1:155196685..155197597,2	Hela-S3	cervix:
2	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:
3	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
4	chr1:70877206..70877981-chr10:52383708..52384377,2	Hela-S3	cervix:
5	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
6	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
7	chr1:70779446..70781152-chr1:70876074..70878497,2	MCF-7	breast:
8	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000050628	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10465863	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs11209599	0.88[CEU][hapmap]
rs11209600	0.88[CEU][hapmap];0.89[AMR][1000 genomes]
rs11209602	0.87[AMR][1000 genomes]
rs11209603	0.83[AMR][1000 genomes]
rs11209608	0.86[AMR][1000 genomes]
rs11209611	0.88[YRI][hapmap];0.91[AMR][1000 genomes]
rs12028257	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs12031053	0.88[CEU][hapmap];0.89[AMR][1000 genomes]
rs12034101	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12036256	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs12037272	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs12042565	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12565458	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565460	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1327873	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131285	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1969953	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs4560989	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs4650038	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs4650041	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs4650047	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211824	0.89[AMR][1000 genomes]
rs58997663	0.86[AMR][1000 genomes]
rs59821213	0.89[AMR][1000 genomes]
rs60602940	0.82[AMR][1000 genomes]
rs61122312	0.88[AMR][1000 genomes]
rs61587863	0.86[AMR][1000 genomes]
rs61678482	0.89[AMR][1000 genomes]
rs6686181	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs72678630	0.89[AMR][1000 genomes]
rs72678644	0.89[AMR][1000 genomes]
rs72678645	0.89[AMR][1000 genomes]
rs72678646	0.91[AMR][1000 genomes]
rs72680732	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539544	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs768433	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs998523	0.88[CEU][hapmap];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12030275	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs12030275	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70875600-70878000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:70875800-70877800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:70875800-70878800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:70875800-70878800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:70875800-70879000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr1:70875800-70879000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:70875800-70879000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:70875800-70879800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:70875800-70880000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:70876000-70877800	Active TSS	Fetal Brain Male	brain
11	chr1:70876000-70877800	Active TSS	Stomach Mucosa	stomach
12	chr1:70876000-70878000	Bivalent/Poised TSS	HepG2	liver
13	chr1:70876000-70878200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:70876000-70878200	Active TSS	Aorta	Aorta
17	chr1:70876000-70878200	Active TSS	Colonic Mucosa	Colon
18	chr1:70876000-70878200	Active TSS	Psoas Muscle	Psoas
19	chr1:70876000-70878200	Active TSS	GM12878-XiMat	blood
20	chr1:70876000-70878400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr1:70876000-70878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:70876000-70878400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:70876000-70878400	Active TSS	Fetal Intestine Large	intestine
24	chr1:70876000-70878600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:70876000-70878600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:70876000-70878600	Active TSS	Ovary	ovary
27	chr1:70876000-70878600	Active TSS	Right Atrium	heart
28	chr1:70876000-70878600	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:70876000-70878800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:70876000-70878800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:70876000-70878800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:70876000-70878800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:70876000-70878800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:70876000-70878800	Active TSS	Brain Substantia Nigra	brain
35	chr1:70876000-70878800	Active TSS	Right Ventricle	heart
36	chr1:70876000-70879000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr1:70876000-70879000	Active TSS	K562	blood
38	chr1:70876200-70877800	Active TSS	Brain Hippocampus Middle	brain
39	chr1:70876200-70877800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr1:70876200-70877800	Active TSS	Fetal Heart	heart
41	chr1:70876200-70877800	Active TSS	Fetal Intestine Small	intestine
42	chr1:70876200-70878000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:70876200-70878000	Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:70876200-70878000	Active TSS	Fetal Muscle Leg	muscle
45	chr1:70876200-70878000	Active TSS	Stomach Smooth Muscle	stomach
46	chr1:70876200-70878000	Active TSS	A549	lung
47	chr1:70876200-70878200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr1:70876200-70878200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:70876200-70878200	Active TSS	Brain Angular Gyrus	brain
50	chr1:70876200-70878400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links