Variant report

Variant	rs17397949
Chromosome Location	chr3:99606325-99606326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:58636264..58638739-chr3:99605809..99607962,2	MCF-7	breast:

Extended variants
information (count: 34 )
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]
rs17778707	1.00[AMR][1000 genomes]
rs17778804	1.00[AMR][1000 genomes]
rs17779605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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: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:21 , 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	chr3:99603400-99609400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:99603600-99611200	Weak transcription	Psoas Muscle	Psoas
9	chr3:99604000-99612600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:99604000-99613200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:99604000-99614400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:99604400-99609000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:99604400-99614000	Weak transcription	HUVEC	blood vessel
14	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
15	chr3:99605000-99609200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:99605000-99609600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:99605000-99613600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:99605000-99614600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:99605200-99608800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:99605200-99613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:99605400-99611000	Weak transcription	HepG2	liver

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