Variant report

Variant	rs3845406
Chromosome Location	chr1:180611883-180611884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180611289..180612983-chr1:180987142..180989197,2	K562	blood:
2	chr1:180600633..180603111-chr1:180610000..180612766,3	K562	blood:
3	chr1:180603575..180607305-chr1:180609187..180612669,3	MCF-7	breast:
4	chr1:180600492..180602685-chr1:180608487..180613245,4	MCF-7	breast:
5	chr1:180611817..180614490-chr1:180617185..180619103,2	K562	blood:
6	chr1:180603512..180606287-chr1:180609976..180612576,4	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10798785	0.80[ASN][1000 genomes]
rs10914096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs12118646	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1339768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap]
rs1970404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs2331626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2331886	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.84[TSI][hapmap]
rs2944259	0.84[CEU][hapmap]
rs2944262	0.89[CEU][hapmap]
rs3002113	0.89[CEU][hapmap]
rs3002114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs3002116	0.89[CEU][hapmap]
rs3002117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3002123	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap]
rs3753202	0.95[ASN][1000 genomes]
rs3819951	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3819953	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3843278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs3856058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4083591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4589068	0.90[EUR][1000 genomes]
rs4651073	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs6659368	0.81[EUR][1000 genomes]
rs6661105	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs7514404	1.00[CEU][hapmap]
rs7524547	0.81[YRI][hapmap]
rs7541650	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs7548318	0.89[CEU][hapmap]
rs7550031	0.89[CEU][hapmap]
rs9425881	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs9970145	0.91[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs9970363	0.91[CHB][hapmap];0.80[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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180615800	Weak transcription	Lung	lung
2	chr1:180602000-180618800	Weak transcription	Pancreas	Pancrea
3	chr1:180602000-180645200	Weak transcription	Gastric	stomach
4	chr1:180602400-180612400	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:180602400-180612600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:180603000-180614800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:180603200-180612000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:180603200-180614400	Weak transcription	Primary B cells from cord blood	blood
9	chr1:180603200-180615200	Weak transcription	HSMM	muscle
10	chr1:180603200-180615800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:180603200-180616400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:180603200-180622400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:180603400-180613000	Weak transcription	Ovary	ovary
14	chr1:180603400-180614800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:180603400-180615400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:180603400-180615600	Weak transcription	HUVEC	blood vessel
17	chr1:180603400-180617000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:180603400-180619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:180603600-180612400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:180603600-180612800	Weak transcription	Aorta	Aorta
21	chr1:180603600-180626400	Weak transcription	Fetal Lung	lung
22	chr1:180603800-180612800	Weak transcription	Primary T cells from cord blood	blood
23	chr1:180603800-180613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:180603800-180614600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:180604000-180613200	Weak transcription	Brain Germinal Matrix	brain
26	chr1:180604000-180623200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:180604800-180617000	Weak transcription	Dnd41	blood
28	chr1:180605000-180612400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:180605600-180612600	Weak transcription	HMEC	breast
30	chr1:180605600-180625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:180605800-180613200	Weak transcription	Fetal Brain Female	brain
32	chr1:180605800-180615000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:180605800-180622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:180605800-180625000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:180606000-180612800	Weak transcription	Right Ventricle	heart
36	chr1:180606000-180614000	Weak transcription	Left Ventricle	heart
37	chr1:180606000-180618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:180607000-180612800	Weak transcription	Fetal Brain Male	brain
39	chr1:180608200-180617000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:180608600-180615600	Enhancers	Fetal Heart	heart
41	chr1:180609800-180614800	Weak transcription	Small Intestine	intestine
42	chr1:180609800-180625800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:180610000-180612200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:180610000-180612400	Weak transcription	A549	lung
45	chr1:180610000-180612600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:180610000-180615400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:180610200-180612800	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr1:180610200-180617000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:180610600-180614800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:180611200-180615400	Genic enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links