Variant report

Variant	rs3861100
Chromosome Location	chr12:50599219-50599220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50598607-50599741	U87	brain:	n/a	n/a
2	POLR2A	chr12:50599137-50599711	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50596300..50599334-chr12:50605728..50608989,3	MCF-7	breast:
2	chr12:50597580..50599392-chr12:50600768..50603210,2	MCF-7	breast:
3	chr12:50597958..50602856-chr12:50604694..50610518,6	K562	blood:
4	chr12:50596667..50602931-chr12:50613575..50616735,6	K562	blood:
5	chr12:50598358..50601280-chr12:50607490..50609263,3	K562	blood:

No data

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10506292	0.84[ASN][1000 genomes]
rs10783344	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783349	0.83[EUR][1000 genomes]
rs10783350	0.81[EUR][1000 genomes]
rs10783353	0.81[ASN][1000 genomes]
rs10876013	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876014	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876015	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876016	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876017	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876018	0.81[EUR][1000 genomes]
rs10876023	0.83[ASN][1000 genomes]
rs10876028	0.82[ASN][1000 genomes]
rs11169314	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169315	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169317	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169319	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169322	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169331	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169332	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169335	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169339	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169345	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169347	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169348	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169349	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169350	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169351	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169357	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169359	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169360	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169367	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169369	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169370	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169371	0.82[EUR][1000 genomes]
rs11169373	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169374	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169375	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169376	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169377	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169379	0.81[EUR][1000 genomes]
rs11169390	0.83[ASN][1000 genomes]
rs11169391	0.82[ASN][1000 genomes]
rs11169395	0.81[ASN][1000 genomes]
rs11836169	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11838347	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12299758	0.84[ASN][1000 genomes]
rs12303082	0.83[ASN][1000 genomes]
rs12312177	0.81[ASN][1000 genomes]
rs12422417	0.83[ASN][1000 genomes]
rs12424691	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424713	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424876	0.81[ASN][1000 genomes]
rs12425229	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425705	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12426444	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12811291	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814094	0.83[ASN][1000 genomes]
rs12821454	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12823506	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12828340	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12832940	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362983	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17124562	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1972611	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1984993	0.84[ASN][1000 genomes]
rs2009072	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2111988	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302900	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2358539	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28628775	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34039674	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34614542	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34825838	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34849043	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34858415	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34894919	0.81[ASN][1000 genomes]
rs35209607	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35535298	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35663729	0.80[EUR][1000 genomes]
rs35768991	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35878271	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35933908	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36017775	0.80[ASN][1000 genomes]
rs3812825	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348979	0.83[ASN][1000 genomes]
rs4421818	0.83[ASN][1000 genomes]
rs4768855	0.81[ASN][1000 genomes]
rs4768872	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768949	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580730	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580735	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580736	0.84[EUR][1000 genomes]
rs6580737	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580738	0.84[EUR][1000 genomes]
rs6580739	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580740	0.82[EUR][1000 genomes]
rs6580741	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67138019	0.87[EUR][1000 genomes]
rs7132551	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135777	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71465002	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295847	0.84[ASN][1000 genomes]
rs7296291	0.84[ASN][1000 genomes]
rs7302363	0.83[ASN][1000 genomes]
rs7304445	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7305995	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308095	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308885	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310541	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311378	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311491	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311973	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312252	0.84[ASN][1000 genomes]
rs7314465	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7315871	0.81[EUR][1000 genomes]
rs7315955	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7399343	0.81[EUR][1000 genomes]
rs7485486	0.82[EUR][1000 genomes]
rs7486747	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7488682	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7489214	0.81[EUR][1000 genomes]
rs7953953	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7956468	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7974648	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979830	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980911	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9668187	0.81[ASN][1000 genomes]
rs9705460	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9739363	0.83[ASN][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3861100	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs3861100	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
5	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
6	chr12:50582400-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
8	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
11	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:50586000-50599600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:50587800-50599800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:50588000-50599800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:50588400-50599600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:50588400-50600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:50588400-50600600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:50588400-50600600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:50589400-50599800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:50589400-50599800	Strong transcription	GM12878-XiMat	blood
22	chr12:50589400-50600800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:50590600-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:50590600-50600200	Strong transcription	Fetal Thymus	thymus
25	chr12:50590800-50599800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:50590800-50600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:50591000-50600200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:50591000-50603000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:50591600-50600000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:50591600-50615600	Weak transcription	HepG2	liver
31	chr12:50592000-50599400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:50592000-50600200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr12:50593400-50614200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:50593400-50614200	Weak transcription	Fetal Brain Male	brain
35	chr12:50593400-50614600	Weak transcription	Esophagus	oesophagus
36	chr12:50594000-50599800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:50594400-50599800	Strong transcription	Rectal Smooth Muscle	rectum
38	chr12:50595600-50599800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:50595600-50600600	Strong transcription	Primary T cells from cord blood	blood
40	chr12:50595800-50600800	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:50596200-50599600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:50596200-50613400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:50596400-50600600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:50596400-50600800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:50596600-50599400	Genic enhancers	NHEK	skin
46	chr12:50596600-50600600	Strong transcription	HSMMtube	muscle
47	chr12:50596600-50604600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:50596600-50605400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:50596600-50607200	Strong transcription	Fetal Intestine Small	intestine
50	chr12:50596800-50599800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links