Variant report

Variant	rs3816832
Chromosome Location	chr3:112727307-112727308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112709111..112712767-chr3:112725826..112728376,3	K562	blood:
2	chr3:112726403..112732813-chr3:112735056..112739637,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD200R1-1	chr3:112727018-112727647	NONHSAT091203

Variant related genes	Relation type
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000240057	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11920110	1.00[AMR][1000 genomes]
rs16860242	0.82[CHB][hapmap]
rs2306858	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732813	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732814	0.87[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3736593	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755743	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57163779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57916867	0.97[ASN][1000 genomes]
rs58720412	1.00[AMR][1000 genomes]
rs59998761	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60626674	0.95[ASN][1000 genomes]
rs6770507	0.82[CHB][hapmap]
rs72952158	0.95[ASN][1000 genomes]
rs72952159	1.00[AMR][1000 genomes]
rs72952160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72952161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72952168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952169	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952172	0.98[ASN][1000 genomes]
rs72952182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72952188	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952192	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651481	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864286	0.82[CHB][hapmap]

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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription 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 miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112710400-112737400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:112711400-112736600	Weak transcription	Stomach Mucosa	stomach
3	chr3:112712200-112736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:112712400-112736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:112712800-112736600	Weak transcription	Fetal Heart	heart
6	chr3:112714400-112736800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:112715000-112735800	Strong transcription	Primary B cells from cord blood	blood
8	chr3:112715200-112736000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr3:112715600-112734600	Strong transcription	Liver	Liver
10	chr3:112715600-112736600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:112715600-112736600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112715800-112735800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112715800-112736000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:112715800-112736200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:112715800-112736800	Strong transcription	Placenta	Placenta
16	chr3:112716000-112736000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:112716000-112736600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:112716200-112735800	Strong transcription	A549	lung
19	chr3:112716400-112735600	Strong transcription	Adipose Nuclei	Adipose
20	chr3:112716400-112736400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:112716400-112736400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:112716800-112729200	Strong transcription	Fetal Lung	lung
23	chr3:112716800-112734400	Strong transcription	GM12878-XiMat	blood
24	chr3:112716800-112735800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:112716800-112736200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:112716800-112736400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:112716800-112736400	Strong transcription	NH-A	brain
28	chr3:112716800-112736600	Strong transcription	Osteobl	bone
29	chr3:112716800-112736800	Strong transcription	HSMM	muscle
30	chr3:112717000-112729600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:112717000-112729600	Strong transcription	Fetal Intestine Large	intestine
32	chr3:112717000-112736400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:112717200-112728000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:112717200-112736000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:112717200-112736200	Strong transcription	HMEC	breast
36	chr3:112717400-112733200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr3:112718400-112736200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:112718600-112728000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:112718600-112729400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:112718600-112735800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:112719600-112728000	Strong transcription	Hela-S3	cervix
42	chr3:112719800-112729600	Strong transcription	Brain Anterior Caudate	brain
43	chr3:112720000-112727800	Strong transcription	HUVEC	blood vessel
44	chr3:112720000-112736400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:112720400-112730000	Strong transcription	Fetal Kidney	kidney
46	chr3:112720800-112729800	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:112721000-112727400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:112721000-112729600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:112721000-112729800	Strong transcription	HepG2	liver
50	chr3:112721200-112728600	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links