Variant report

Variant	rs7342929
Chromosome Location	chr17:28612202-28612203
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:28608757..28613119-chr17:28617171..28619214,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108578	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1050565	0.94[JPT][hapmap]
rs11867581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939390	0.94[JPT][hapmap]
rs12949747	0.94[JPT][hapmap]
rs13341611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1487971	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17767256	0.94[JPT][hapmap]
rs2321705	0.86[ASN][1000 genomes]
rs3103305	0.86[ASN][1000 genomes]
rs3110094	0.83[ASN][1000 genomes]
rs3110095	0.83[ASN][1000 genomes]
rs3110452	0.94[JPT][hapmap]
rs3110453	0.86[ASN][1000 genomes]
rs33980254	0.94[JPT][hapmap]
rs3764449	0.94[JPT][hapmap]
rs3794806	0.94[JPT][hapmap]
rs3816828	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505165	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505171	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505173	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208052	0.94[JPT][hapmap]
rs7210085	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214248	0.94[JPT][hapmap]
rs7214991	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7215330	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7223821	0.94[JPT][hapmap]
rs7342921	0.94[JPT][hapmap]
rs8072345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8073378	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080300	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896548	0.86[EUR][1000 genomes];0.91[ASN][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	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28566600-28618000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:28571400-28618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:28573800-28615400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr17:28574000-28616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:28576200-28618000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:28579200-28616200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:28583000-28616600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr17:28583000-28616600	Strong transcription	Fetal Thymus	thymus
9	chr17:28583600-28616400	Strong transcription	Dnd41	blood
10	chr17:28586000-28617400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:28588200-28615000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:28589200-28616400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:28589600-28616600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:28591200-28613400	Weak transcription	Pancreas	Pancrea
15	chr17:28591200-28617200	Weak transcription	Hela-S3	cervix
16	chr17:28591800-28616400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:28592400-28617200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:28592600-28615200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:28596600-28616800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:28598000-28616600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:28599800-28616800	Strong transcription	A549	lung
22	chr17:28600200-28612400	Weak transcription	Fetal Brain Male	brain
23	chr17:28600200-28613400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr17:28600400-28617200	Weak transcription	Psoas Muscle	Psoas
25	chr17:28600600-28618000	Weak transcription	Gastric	stomach
26	chr17:28601000-28612400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:28601000-28617200	Weak transcription	Small Intestine	intestine
28	chr17:28601200-28612400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:28601200-28612400	Weak transcription	Esophagus	oesophagus
30	chr17:28601200-28613200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:28601400-28613000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr17:28602000-28612800	Weak transcription	Right Ventricle	heart
33	chr17:28602200-28614000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:28602600-28615000	Strong transcription	Adipose Nuclei	Adipose
35	chr17:28602600-28617200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr17:28603200-28615000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr17:28603200-28616400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:28604200-28616200	Strong transcription	Placenta	Placenta
39	chr17:28604600-28617200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr17:28605200-28615000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:28605200-28616600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:28605600-28615000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:28605600-28615000	Strong transcription	Fetal Brain Female	brain
44	chr17:28605600-28616000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:28605600-28616600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:28605600-28616600	Strong transcription	Fetal Intestine Large	intestine
47	chr17:28605600-28616600	Strong transcription	Fetal Muscle Leg	muscle
48	chr17:28605600-28616600	Strong transcription	Left Ventricle	heart
49	chr17:28605600-28617000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:28605600-28617200	Weak transcription	Fetal Heart	heart

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