Variant report

Variant	rs17779605
Chromosome Location	chr3:99602902-99602903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99601088..99603478-chr3:99611897..99614954,3	MCF-7	breast:
2	chr3:99596053..99600789-chr3:99601531..99605674,5	MCF-7	breast:
3	chr3:99601766..99603960-chr3:99724495..99726434,2	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: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs15890	1.00[AMR][1000 genomes]
rs17313676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314245	1.00[EUR][1000 genomes]
rs17314280	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[EUR][1000 genomes]
rs17393080	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[AMR][1000 genomes]
rs2035400	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]
rs6762809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762871	1.00[EUR][1000 genomes]
rs6781780	1.00[EUR][1000 genomes]
rs6784150	1.00[EUR][1000 genomes]
rs6788807	1.00[EUR][1000 genomes]
rs6790187	1.00[EUR][1000 genomes]
rs6794130	1.00[EUR][1000 genomes]
rs6794365	1.00[EUR][1000 genomes]
rs6803576	1.00[AMR][1000 genomes]
rs6807137	1.00[EUR][1000 genomes]
rs6807615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7619738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626310	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]
rs9756455	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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99595400-99603000	Weak transcription	Stomach Mucosa	stomach
2	chr3:99595400-99603400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:99595400-99603400	Weak transcription	Small Intestine	intestine
4	chr3:99595400-99608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:99595600-99603200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:99595600-99607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:99595600-99612800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:99595800-99603200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:99596000-99603000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:99596000-99603200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:99596600-99614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:99597000-99603400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:99597200-99603000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:99597200-99603400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:99597200-99614200	Weak transcription	HMEC	breast
16	chr3:99597800-99603400	Weak transcription	GM12878-XiMat	blood
17	chr3:99600200-99603200	Enhancers	HUVEC	blood vessel
18	chr3:99600600-99603400	Weak transcription	Brain Anterior Caudate	brain
19	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
20	chr3:99601400-99603200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:99601600-99603400	Weak transcription	Adipose Nuclei	Adipose
22	chr3:99601800-99603200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:99601800-99604800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:99602000-99604600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:99602000-99605400	Enhancers	HepG2	liver
26	chr3:99602400-99604200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:99602600-99604200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:99602600-99604600	Enhancers	Primary T cells from cord blood	blood
29	chr3:99602600-99604800	Enhancers	Fetal Intestine Large	intestine
30	chr3:99602600-99605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:99602800-99603000	Enhancers	Psoas Muscle	Psoas
32	chr3:99602800-99604000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:99602800-99604000	Enhancers	K562	blood
34	chr3:99602800-99604200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:99602800-99604200	Enhancers	NHEK	skin
36	chr3:99602800-99604600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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