Variant report

Variant	rs9871175
Chromosome Location	chr3:52945930-52945931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52940294..52941898-chr3:52943959..52945986,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10865977	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130331	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715347	0.81[EUR][1000 genomes]
rs11915546	0.80[EUR][1000 genomes]
rs11922975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487379	0.88[EUR][1000 genomes]
rs12492391	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12629687	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638968	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13072537	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2336558	0.81[EUR][1000 genomes]
rs2336664	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2336667	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336668	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821873	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4350911	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687562	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4687679	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687680	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4687682	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687683	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687684	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687687	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687689	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56019197	0.80[EUR][1000 genomes]
rs56383738	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253583	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6764322	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769789	0.81[EUR][1000 genomes]
rs6773650	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795646	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7612624	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7620690	0.83[EUR][1000 genomes]
rs7626551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630552	0.83[EUR][1000 genomes]
rs9810807	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825230	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9836499	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9850563	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9860296	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9865248	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866243	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880619	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9880978	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9985365	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9871175	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9871175	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9871175	ITIH4-AS1	cis	lung	GTEx
rs9871175	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
2	chr3:52932000-52946400	Weak transcription	Esophagus	oesophagus
3	chr3:52932000-52953400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
5	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:52932200-52946000	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:52932200-52948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:52932200-52948800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:52932200-52951400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:52932200-52952800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:52932200-52953600	Weak transcription	Right Ventricle	heart
14	chr3:52932200-52953800	Weak transcription	Ovary	ovary
15	chr3:52932200-52961400	Weak transcription	HSMMtube	muscle
16	chr3:52932200-52961800	Weak transcription	A549	lung
17	chr3:52932200-52963000	Weak transcription	Stomach Mucosa	stomach
18	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:52932200-52967800	Weak transcription	HSMM	muscle
20	chr3:52932200-52968600	Weak transcription	Osteobl	bone
21	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
23	chr3:52932400-52946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:52932400-52946400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:52932400-52946600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:52932400-52947000	Weak transcription	Fetal Heart	heart
27	chr3:52932400-52948200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:52932400-52953000	Weak transcription	Brain Angular Gyrus	brain
29	chr3:52932400-52953400	Weak transcription	Fetal Kidney	kidney
30	chr3:52932400-52968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:52932400-52968600	Weak transcription	NHDF-Ad	bronchial
32	chr3:52932400-52968800	Weak transcription	NHEK	skin
33	chr3:52935600-52968600	Strong transcription	Dnd41	blood
34	chr3:52936600-52947000	Weak transcription	Fetal Brain Female	brain
35	chr3:52937200-52959800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:52938000-52959000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:52938400-52946400	Weak transcription	Fetal Lung	lung
38	chr3:52939400-52946400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:52939400-52946400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52939400-52947000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:52939400-52947000	Weak transcription	HepG2	liver
42	chr3:52939400-52953000	Weak transcription	Aorta	Aorta
43	chr3:52939600-52953400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:52939600-52961200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:52940000-52947400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:52940200-52949000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:52940200-52953400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:52940600-52946400	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:52940600-52946800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:52941000-52947000	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links