Variant report

Variant	rs17313676
Chromosome Location	chr3:99644551-99644552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99639154..99641723-chr3:99643232..99645940,2	MCF-7	breast:
2	chr3:99638906..99644679-chr3:99646570..99651799,7	K562	blood:
3	chr3:99639074..99641020-chr3:99643167..99645539,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs15890	1.00[AMR][1000 genomes]
rs16841712	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs17314245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314977	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17314998	1.00[ASW][hapmap]
rs17338576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17392822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17393080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17397949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778707	1.00[AMR][1000 genomes]
rs17778804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17779605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035400	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41444055	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs41477051	0.89[AFR][1000 genomes]
rs6762809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762871	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6764470	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6765822	0.89[AFR][1000 genomes]
rs6772519	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6778756	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6781780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6784150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6787184	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6788807	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6789840	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6790187	1.00[EUR][1000 genomes]
rs6791426	1.00[ASW][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6794130	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6794365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6801514	1.00[YRI][hapmap]
rs6803576	1.00[AMR][1000 genomes]
rs6805703	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6805834	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6807137	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6807615	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808420	1.00[YRI][hapmap]
rs7611313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626214	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7626310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628458	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7646221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648943	1.00[EUR][1000 genomes]
rs766777	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs768527	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9756455	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99630600-99644600	Weak transcription	NH-A	brain
3	chr3:99634400-99647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:99640000-99644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:99640000-99648400	Weak transcription	HSMMtube	muscle
6	chr3:99640200-99648400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:99640200-99648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:99640400-99644600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:99640400-99644600	Weak transcription	Spleen	Spleen
10	chr3:99640400-99644600	Weak transcription	HSMM	muscle
11	chr3:99640400-99645400	Enhancers	HepG2	liver
12	chr3:99640400-99645600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:99640400-99646200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:99640400-99647000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:99640400-99648400	Weak transcription	Gastric	stomach
16	chr3:99640400-99648600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:99640400-99656000	Weak transcription	GM12878-XiMat	blood
18	chr3:99640400-99656600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:99640400-99656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:99641000-99648200	Weak transcription	Psoas Muscle	Psoas
21	chr3:99641200-99646600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:99641200-99648400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:99641400-99654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:99642200-99647000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:99642200-99654000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:99642400-99645400	Enhancers	Fetal Intestine Large	intestine
27	chr3:99643200-99646600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:99643800-99644800	Enhancers	Brain Germinal Matrix	brain
29	chr3:99643800-99644800	Enhancers	Esophagus	oesophagus
30	chr3:99643800-99646600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:99643800-99646600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr3:99643800-99646800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:99644000-99645200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:99644000-99645200	Enhancers	Fetal Intestine Small	intestine
35	chr3:99644000-99645400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:99644000-99645400	Enhancers	Colon Smooth Muscle	Colon
37	chr3:99644000-99649800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:99644200-99644600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:99644200-99644800	Enhancers	Adipose Nuclei	Adipose
40	chr3:99644200-99644800	Enhancers	Fetal Muscle Leg	muscle
41	chr3:99644200-99644800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:99644200-99645000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr3:99644200-99645200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:99644200-99645200	Enhancers	Small Intestine	intestine
45	chr3:99644200-99645200	Enhancers	Stomach Mucosa	stomach
46	chr3:99644200-99645200	Enhancers	NHLF	lung
47	chr3:99644200-99645400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr3:99644200-99645400	Enhancers	Rectal Smooth Muscle	rectum
49	chr3:99644200-99645400	Enhancers	NHDF-Ad	bronchial
50	chr3:99644200-99645600	Enhancers	NHEK	skin

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