Variant report

Variant	rs7619738
Chromosome Location	chr3:99604185-99604186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99596053..99600789-chr3:99601531..99605674,5	MCF-7	breast:
2	chr3:99603110..99605515-chr3:99787025..99789865,2	MCF-7	breast:
3	chr3:99603421..99605877-chr3:99613161..99615005,2	MCF-7	breast:
4	chr3:99602517..99605057-chr7:140621979..140624575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs15890	1.00[AMR][1000 genomes]
rs16841650	1.00[YRI][hapmap]
rs16841653	1.00[YRI][hapmap]
rs16841712	1.00[YRI][hapmap]
rs17313676	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314245	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314280	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314977	1.00[EUR][1000 genomes]
rs17338576	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17392822	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17393080	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17397949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778707	1.00[AMR][1000 genomes]
rs17778804	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17779605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035400	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41444055	1.00[YRI][hapmap]
rs6762809	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762871	1.00[EUR][1000 genomes]
rs6764470	1.00[YRI][hapmap]
rs6772519	1.00[YRI][hapmap]
rs6781780	1.00[EUR][1000 genomes]
rs6784150	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6787184	1.00[YRI][hapmap]
rs6788807	1.00[EUR][1000 genomes]
rs6789840	1.00[YRI][hapmap]
rs6790187	1.00[EUR][1000 genomes]
rs6791426	1.00[YRI][hapmap]
rs6794130	1.00[EUR][1000 genomes]
rs6794365	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6803576	1.00[AMR][1000 genomes]
rs6805703	1.00[YRI][hapmap]
rs6807137	1.00[EUR][1000 genomes]
rs6807615	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808420	1.00[YRI][hapmap]
rs7611313	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7626214	1.00[YRI][hapmap]
rs7626310	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628458	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7646221	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648943	1.00[EUR][1000 genomes]
rs766777	1.00[EUR][1000 genomes]
rs768527	1.00[YRI][hapmap]
rs9756455	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][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	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
3	nsv822194	chr3:99600260-99604375	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99595400-99608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:99595600-99607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:99595600-99612800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:99596600-99614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99597200-99614200	Weak transcription	HMEC	breast
6	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
7	chr3:99601800-99604800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:99602000-99604600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:99602000-99605400	Enhancers	HepG2	liver
10	chr3:99602400-99604200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:99602600-99604200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:99602600-99604600	Enhancers	Primary T cells from cord blood	blood
13	chr3:99602600-99604800	Enhancers	Fetal Intestine Large	intestine
14	chr3:99602600-99605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:99602800-99604200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:99602800-99604200	Enhancers	NHEK	skin
17	chr3:99602800-99604600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:99603000-99604200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:99603000-99604200	Enhancers	Duodenum Mucosa	Duodenum
20	chr3:99603000-99604400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:99603000-99605400	Enhancers	Stomach Mucosa	stomach
22	chr3:99603200-99604200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:99603200-99604200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:99603400-99604200	Enhancers	Small Intestine	intestine
25	chr3:99603400-99604400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:99603400-99604800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr3:99603400-99605000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:99603400-99605400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:99603400-99609400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:99603600-99604200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr3:99603600-99611200	Weak transcription	Psoas Muscle	Psoas
32	chr3:99603800-99604400	Enhancers	HUVEC	blood vessel
33	chr3:99603800-99604600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:99603800-99605200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:99604000-99604400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:99604000-99604600	Weak transcription	K562	blood
37	chr3:99604000-99612600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:99604000-99613200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:99604000-99614400	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links