Variant report

Variant	rs3736905
Chromosome Location	chr1:67392614-67392615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:67392172-67392667	K562	blood:	n/a	chr1:67392225-67392239 chr1:67392223-67392237 chr1:67392222-67392236 chr1:67392227-67392238 chr1:67392226-67392237 chr1:67392224-67392237 chr1:67392226-67392236 chr1:67392224-67392238 chr1:67392226-67392240
2	CEBPB	chr1:67392419-67392756	K562	blood:	n/a	chr1:67392577-67392590 chr1:67392677-67392694

No.	Distal block	Cell Line	Cell type
1	chr1:67389047..67393171-chr1:67393255..67399137,11	MCF-7	breast:
2	chr1:65608373..65610541-chr1:67391827..67393625,2	MCF-7	breast:
3	chr1:67385997..67392679-chr1:67394416..67400305,9	MCF-7	breast:
4	chr1:67390720..67392859-chr1:67459230..67461663,2	K562	blood:

Variant related genes	Relation type
WDR78	TF binding region
MIER1	TF binding region
ENSG00000198160	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10749766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10789219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889651	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1118392	0.91[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs11208971	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208973	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11208979	0.90[JPT][hapmap]
rs1121824	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12041926	0.90[JPT][hapmap]
rs12044278	0.92[JPT][hapmap]
rs12131222	0.92[JPT][hapmap]
rs12137403	0.90[JPT][hapmap]
rs12562761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12742428	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1570838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17497828	0.90[JPT][hapmap]
rs1925408	0.90[JPT][hapmap]
rs1925409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925411	0.92[JPT][hapmap]
rs1925413	0.92[JPT][hapmap]
rs2025608	0.92[JPT][hapmap]
rs2065000	0.92[JPT][hapmap]
rs2065001	0.90[JPT][hapmap]
rs2065002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2182143	0.90[JPT][hapmap]
rs2755241	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2755242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2755243	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2755244	0.90[JPT][hapmap]
rs2755245	0.90[JPT][hapmap]
rs2755246	0.90[JPT][hapmap]
rs2755250	0.92[JPT][hapmap]
rs2755251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2755253	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2755254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2755256	0.82[JPT][hapmap]
rs2755266	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2755270	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2755271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2815349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2815351	0.90[JPT][hapmap]
rs2815355	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2815359	0.90[JPT][hapmap]
rs2815360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815361	0.90[JPT][hapmap]
rs2815362	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815364	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815365	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815366	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815367	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2815368	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2815370	0.90[JPT][hapmap]
rs2815371	0.90[JPT][hapmap]
rs2815374	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2985795	0.92[JPT][hapmap]
rs2985797	0.90[JPT][hapmap]
rs2985818	0.90[JPT][hapmap]
rs2985821	0.92[JPT][hapmap]
rs2985822	0.90[JPT][hapmap]
rs2985824	0.90[JPT][hapmap]
rs2985825	0.90[JPT][hapmap]
rs2985826	0.92[JPT][hapmap]
rs3008848	0.90[JPT][hapmap]
rs3008853	0.92[JPT][hapmap]
rs3008854	0.92[JPT][hapmap]
rs3008855	0.90[JPT][hapmap]
rs3008858	0.92[JPT][hapmap]
rs3008871	0.81[JPT][hapmap]
rs3008892	0.90[JPT][hapmap]
rs3929738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4486425	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4570393	0.85[EUR][1000 genomes]
rs4581250	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4582760	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4620509	0.92[JPT][hapmap]
rs4655658	0.92[JPT][hapmap]
rs4655660	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655661	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655663	0.90[JPT][hapmap]
rs6657065	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673462	0.92[JPT][hapmap]
rs912797	0.90[JPT][hapmap]

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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv871720	chr1:67357596-67435161	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv947266	chr1:67358868-67399427	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3448405	chr1:67360980-67393830	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3736905	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL
rs3736905	MIER1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67388800-67392800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:67389600-67392800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:67389600-67394000	Active TSS	K562	blood
4	chr1:67391800-67393000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:67391800-67393400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:67391800-67395000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:67391800-67395400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:67392000-67392800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:67392000-67392800	Enhancers	Brain Germinal Matrix	brain
10	chr1:67392000-67392800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:67392000-67393000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:67392000-67393000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:67392000-67393000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:67392000-67393000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:67392000-67393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:67392000-67393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:67392000-67393000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:67392000-67393000	Enhancers	Colon Smooth Muscle	Colon
19	chr1:67392000-67393000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:67392000-67393000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:67392000-67393000	Enhancers	HSMM	muscle
22	chr1:67392000-67393000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr1:67392000-67393200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:67392000-67393200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:67392000-67393200	Enhancers	HepG2	liver
26	chr1:67392000-67394200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:67392000-67394600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:67392000-67394800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:67392000-67394800	Weak transcription	Liver	Liver
30	chr1:67392000-67395000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:67392000-67395000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:67392000-67395000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:67392000-67395000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:67392000-67395000	Weak transcription	Adipose Nuclei	Adipose
35	chr1:67392000-67395000	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:67392000-67395000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:67392000-67395000	Weak transcription	Brain Substantia Nigra	brain
38	chr1:67392000-67395000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:67392000-67395000	Weak transcription	Fetal Brain Female	brain
40	chr1:67392000-67395000	Weak transcription	Fetal Intestine Small	intestine
41	chr1:67392000-67395000	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:67392000-67395000	Weak transcription	Placenta	Placenta
43	chr1:67392000-67395000	Weak transcription	Fetal Thymus	thymus
44	chr1:67392000-67395200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:67392000-67395200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:67392000-67395200	Weak transcription	Fetal Stomach	stomach
47	chr1:67392000-67395200	Weak transcription	Right Ventricle	heart
48	chr1:67392000-67395200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:67392000-67395200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:67392000-67395200	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links