Variant report

Variant	rs7628932
Chromosome Location	chr3:42550323-42550324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:42550180-42550442	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42542738..42545212-chr3:42547259..42551511,4	MCF-7	breast:
2	chr3:42543515..42546582-chr3:42549981..42551633,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC22C-1	chr3:42550304-42550427	ENSG00000232354.3

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1078008	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13321590	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1511955	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17030440	1.00[MEX][hapmap]
rs1876504	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876506	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467424	0.88[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs55886057	1.00[EUR][1000 genomes]
rs56184136	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73082655	0.83[EUR][1000 genomes]
rs7613206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628235	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651400	0.91[EUR][1000 genomes]
rs95923	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9867564	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42544600-42551600	Weak transcription	Pancreas	Pancrea
2	chr3:42544800-42550600	Weak transcription	Right Atrium	heart
3	chr3:42545400-42551400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:42546600-42553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
7	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:42547800-42551000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:42548400-42551000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:42548400-42552400	Enhancers	Colonic Mucosa	Colon
11	chr3:42548600-42550400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:42548600-42550400	Enhancers	Fetal Thymus	thymus
13	chr3:42548600-42550800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:42548600-42550800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:42548600-42553000	Enhancers	Stomach Mucosa	stomach
16	chr3:42548800-42551600	Enhancers	Lung	lung
17	chr3:42548800-42553200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:42549000-42550400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:42549200-42551400	Weak transcription	Left Ventricle	heart
20	chr3:42549200-42551600	Weak transcription	Esophagus	oesophagus
21	chr3:42549200-42551600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:42549400-42555800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:42549600-42550400	Enhancers	Gastric	stomach
25	chr3:42549600-42550800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:42549800-42550400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:42549800-42550600	Weak transcription	Adipose Nuclei	Adipose
28	chr3:42549800-42550600	Weak transcription	Spleen	Spleen
29	chr3:42549800-42550800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr3:42549800-42551400	Weak transcription	Placenta	Placenta
31	chr3:42549800-42551600	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:42549800-42552000	Enhancers	Small Intestine	intestine
33	chr3:42549800-42553000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:42549800-42553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:42549800-42553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:42549800-42557000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:42549800-42560600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:42550000-42550400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:42550000-42550400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:42550000-42550400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:42550000-42556000	Weak transcription	Brain Anterior Caudate	brain
42	chr3:42550000-42560400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:42550200-42550400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:42550200-42550400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:42550200-42550400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:42550200-42550400	Enhancers	Fetal Heart	heart
47	chr3:42550200-42550400	Genic enhancers	Fetal Intestine Large	intestine
48	chr3:42550200-42550600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:42550200-42550800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr3:42550200-42551400	Enhancers	Rectal Mucosa Donor 29	rectum

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