Variant report

Variant	rs35882887
Chromosome Location	chr1:171751666-171751667
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	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:
2	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
3	chr1:171719352..171723049-chr1:171749265..171752646,3	MCF-7	breast:
4	chr1:171729687..171733295-chr1:171747531..171751881,5	K562	blood:
5	chr1:171750053..171752040-chr1:171760205..171763597,3	MCF-7	breast:
6	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
7	chr1:171708496..171713095-chr1:171747641..171752422,13	MCF-7	breast:
8	chr1:171734176..171737844-chr1:171748206..171752284,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236741	Chromatin interaction
ENSG00000117533	Chromatin interaction
ENSG00000232261	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000253060	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045456	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913683	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913684	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12091786	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565176	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12567851	0.87[EUR][1000 genomes]
rs12730717	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742601	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17596025	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17596081	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17649609	0.98[EUR][1000 genomes]
rs17650310	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650340	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes]
rs1801898	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143369	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2181216	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2223602	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2232807	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232813	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232819	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232825	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236894	0.81[EUR][1000 genomes]
rs236897	0.86[EUR][1000 genomes]
rs236898	0.86[EUR][1000 genomes]
rs236899	0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs34320898	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35400839	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35631282	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35674909	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35930163	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36080557	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3891278	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes]
rs56365362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	0.98[EUR][1000 genomes]
rs6675708	0.98[EUR][1000 genomes]
rs6681322	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7522582	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536142	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv522889	chr1:171749665-171755071	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35882887	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171749600-171751800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:171749600-171751800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171749600-171751800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:171749600-171751800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:171749600-171751800	Active TSS	Fetal Kidney	kidney
6	chr1:171749600-171752000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:171749600-171752000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:171749600-171752200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:171749600-171752400	Active TSS	Rectal Smooth Muscle	rectum
10	chr1:171749800-171751800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:171749800-171751800	Active TSS	Brain Angular Gyrus	brain
12	chr1:171749800-171751800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:171749800-171751800	Active TSS	Colonic Mucosa	Colon
14	chr1:171749800-171751800	Active TSS	Fetal Intestine Small	intestine
15	chr1:171749800-171751800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:171749800-171751800	Active TSS	Psoas Muscle	Psoas
17	chr1:171749800-171751800	Active TSS	Right Ventricle	heart
18	chr1:171749800-171751800	Active TSS	HSMM	muscle
19	chr1:171749800-171751800	Active TSS	HSMMtube	muscle
20	chr1:171749800-171751800	Active TSS	NH-A	brain
21	chr1:171749800-171752200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:171749800-171752200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:171749800-171752200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr1:171749800-171752200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr1:171749800-171752200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:171749800-171752400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:171749800-171752400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:171749800-171752600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr1:171750000-171751800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:171750000-171751800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:171750000-171751800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:171750000-171751800	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:171750000-171751800	Active TSS	Colon Smooth Muscle	Colon
34	chr1:171750000-171751800	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr1:171750000-171751800	Active TSS	A549	lung
36	chr1:171750000-171751800	Active TSS	NHLF	lung
37	chr1:171750000-171752000	Active TSS	Brain Germinal Matrix	brain
38	chr1:171750000-171752000	Active TSS	Thymus	Thymus
39	chr1:171750200-171751800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:171750200-171751800	Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:171750200-171751800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:171750200-171751800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:171750200-171751800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:171750200-171751800	Active TSS	Fetal Lung	lung
45	chr1:171750200-171751800	Active TSS	Gastric	stomach
46	chr1:171750200-171751800	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:171750200-171751800	Active TSS	Small Intestine	intestine
48	chr1:171750200-171751800	Active TSS	GM12878-XiMat	blood
49	chr1:171750200-171751800	Active TSS	Hela-S3	cervix
50	chr1:171750200-171751800	Active TSS	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links