Variant report

Variant	rs17764980
Chromosome Location	chr3:45939016-45939017
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	chr3:45888141..45889967-chr3:45938093..45939850,2	K562	blood:
2	chr3:45936711..45939307-chr3:45956614..45959025,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163818	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs13059238	0.86[EUR][1000 genomes]
rs13060287	0.80[EUR][1000 genomes]
rs13063527	1.00[AFR][1000 genomes]
rs13066062	0.90[EUR][1000 genomes]
rs13066516	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13068570	1.00[AFR][1000 genomes]
rs13069079	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13071283	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs13072267	1.00[AFR][1000 genomes]
rs13074382	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs13075528	1.00[AFR][1000 genomes]
rs13075758	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13078739	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs13079869	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs13081151	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13081213	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs13082697	0.80[EUR][1000 genomes]
rs13089554	1.00[AFR][1000 genomes]
rs13089855	0.82[EUR][1000 genomes]
rs13090194	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs13091868	1.00[AFR][1000 genomes]
rs13093179	1.00[AFR][1000 genomes]
rs13095602	1.00[AFR][1000 genomes]
rs13095717	1.00[AFR][1000 genomes]
rs13096741	1.00[AFR][1000 genomes]
rs13097556	0.80[EUR][1000 genomes]
rs13099120	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13433997	0.81[EUR][1000 genomes]
rs1491950	1.00[AFR][1000 genomes]
rs17214952	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs17215008	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17215981	1.00[AFR][1000 genomes]
rs17280623	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs17330872	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17714101	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17714228	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17764831	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1994491	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1994492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1994493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2088690	0.80[EUR][1000 genomes]
rs2088692	0.80[EUR][1000 genomes]
rs2102055	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2171531	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2230322	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2373087	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33910087	0.90[EUR][1000 genomes]
rs34000569	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34047915	1.00[AFR][1000 genomes]
rs34068335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34093271	1.00[AFR][1000 genomes]
rs34127208	1.00[AFR][1000 genomes]
rs34168660	0.80[EUR][1000 genomes]
rs34283240	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34324101	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34339943	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34340587	1.00[AFR][1000 genomes]
rs34381952	0.90[EUR][1000 genomes]
rs34438204	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34442130	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34452002	1.00[AFR][1000 genomes]
rs34460587	1.00[AFR][1000 genomes]
rs34492478	1.00[AFR][1000 genomes]
rs34493660	0.82[EUR][1000 genomes]
rs34518147	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34562820	0.81[EUR][1000 genomes]
rs34584867	0.80[EUR][1000 genomes]
rs34619093	0.81[EUR][1000 genomes]
rs34679077	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34718164	1.00[AFR][1000 genomes]
rs34754340	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34766614	1.00[AFR][1000 genomes]
rs34774687	0.80[EUR][1000 genomes]
rs34836513	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34849862	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34863575	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34901975	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35159820	0.80[EUR][1000 genomes]
rs35161099	0.81[EUR][1000 genomes]
rs35209528	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35280891	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35334665	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35454877	0.80[EUR][1000 genomes]
rs35477280	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35501575	0.91[EUR][1000 genomes]
rs35516580	1.00[AFR][1000 genomes]
rs35525815	0.89[EUR][1000 genomes]
rs35669129	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs35751180	0.81[EUR][1000 genomes]
rs35772789	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35814488	0.80[EUR][1000 genomes]
rs35827997	0.90[EUR][1000 genomes]
rs35831747	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35855315	0.89[EUR][1000 genomes]
rs35883205	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35921206	0.80[EUR][1000 genomes]
rs35930050	0.80[EUR][1000 genomes]
rs36023124	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs36039366	0.90[EUR][1000 genomes]
rs36040135	0.80[EUR][1000 genomes]
rs36057789	1.00[AFR][1000 genomes]
rs36122610	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3851346	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs41289616	0.90[EUR][1000 genomes]
rs41289622	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4362758	0.80[EUR][1000 genomes]
rs4373103	1.00[AFR][1000 genomes]
rs4388012	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs55875328	0.82[EUR][1000 genomes]
rs55920693	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56332428	0.90[EUR][1000 genomes]
rs60019065	0.80[EUR][1000 genomes]
rs61556067	0.82[EUR][1000 genomes]
rs61650989	0.82[EUR][1000 genomes]
rs67200151	0.82[EUR][1000 genomes]
rs6780028	0.80[EUR][1000 genomes]
rs6782814	0.88[EUR][1000 genomes]
rs6785091	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs6790866	0.80[EUR][1000 genomes]
rs6791016	0.80[EUR][1000 genomes]
rs67937868	0.82[EUR][1000 genomes]
rs71325091	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71325092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71325095	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs71325096	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs71325098	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs71325100	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs71325101	0.87[EUR][1000 genomes]
rs71325102	0.89[EUR][1000 genomes]
rs71327003	0.84[EUR][1000 genomes]
rs71327006	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71327007	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71327009	0.81[EUR][1000 genomes]
rs71327010	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71327014	1.00[AFR][1000 genomes]
rs71327015	1.00[AFR][1000 genomes]
rs71327017	1.00[AFR][1000 genomes]
rs71327021	1.00[AFR][1000 genomes]
rs71327023	1.00[AFR][1000 genomes]
rs71327024	1.00[AFR][1000 genomes]
rs71327025	1.00[AFR][1000 genomes]
rs71615437	1.00[AFR][1000 genomes]
rs71615438	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7653372	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs876668	0.80[EUR][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45923400-45948200	Weak transcription	Right Atrium	heart
2	chr3:45925200-45949600	Weak transcription	Pancreas	Pancrea
3	chr3:45925600-45947800	Genic enhancers	Dnd41	blood
4	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
5	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
6	chr3:45934600-45946200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:45935400-45941200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:45935400-45945000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:45936000-45947600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:45936200-45939400	Enhancers	Hela-S3	cervix
11	chr3:45936400-45939200	Enhancers	HMEC	breast
12	chr3:45936600-45940200	Genic enhancers	Thymus	Thymus
13	chr3:45936600-45945800	Weak transcription	Primary B cells from cord blood	blood
14	chr3:45936600-45950200	Genic enhancers	Fetal Thymus	thymus
15	chr3:45936800-45939600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:45936800-45941000	Weak transcription	Primary T cells from cord blood	blood
17	chr3:45936800-45946200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:45937400-45939200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:45937600-45939200	Enhancers	Placenta	Placenta
20	chr3:45937800-45939200	Enhancers	Fetal Stomach	stomach
21	chr3:45937800-45939400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:45937800-45939400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:45937800-45939400	Enhancers	Esophagus	oesophagus
24	chr3:45938200-45939200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:45938200-45941000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:45938400-45939200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:45938400-45939800	Strong transcription	Aorta	Aorta
28	chr3:45938600-45949000	Weak transcription	Small Intestine	intestine
29	chr3:45938800-45939200	Weak transcription	NH-A	brain
30	chr3:45939000-45943000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links