Variant report

Variant	rs1860523
Chromosome Location	chr7:38255339-38255340
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38254875..38255995-chr7:38357724..38359529,9	MCF-7	breast:
2	chr7:38253002..38255460-chr7:38256658..38259135,2	K562	blood:
3	chr7:38255012..38257306-chr7:38260650..38262240,2	K562	blood:
4	chr7:38146750..38147644-chr7:38255037..38256019,2	K562	blood:
5	chr7:38255022..38255645-chr7:38375302..38376120,3	MCF-7	breast:
6	chr7:38146765..38147691-chr7:38255215..38255987,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000211695	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1019179	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10255648	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10260257	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10260281	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10265931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10480165	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs11765477	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11773415	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155081	0.82[YRI][hapmap]
rs12671662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171306	0.91[CHB][hapmap]
rs1860517	0.81[YRI][hapmap]
rs1860519	0.81[YRI][hapmap]
rs2079850	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2191313	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240823	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723736	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59870865	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73128691	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9490	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9801416	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv830964	chr7:38218708-38390518	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1030349	chr7:38227528-38372719	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv538818	chr7:38227528-38372719	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv433041	chr7:38229107-38358728	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv433044	chr7:38238119-38358728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1860523	STARD3NL	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38218600-38259200	Weak transcription	Colonic Mucosa	Colon
2	chr7:38223600-38255600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:38228000-38256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38230200-38259200	Weak transcription	K562	blood
5	chr7:38232800-38256000	Weak transcription	Fetal Brain Male	brain
6	chr7:38236800-38261600	Weak transcription	HMEC	breast
7	chr7:38237200-38255600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:38237600-38258600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:38237800-38261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:38238000-38257000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:38238000-38259200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:38238400-38255400	Weak transcription	Lung	lung
13	chr7:38238600-38268800	Weak transcription	Esophagus	oesophagus
14	chr7:38239200-38255600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:38239200-38256200	Weak transcription	Aorta	Aorta
16	chr7:38239800-38256600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:38245400-38255600	Weak transcription	HepG2	liver
18	chr7:38246600-38255600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:38247400-38255400	Weak transcription	Fetal Brain Female	brain
20	chr7:38247800-38255400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:38249200-38256000	Weak transcription	NHEK	skin
22	chr7:38249200-38259200	Weak transcription	Spleen	Spleen
23	chr7:38249400-38256400	Weak transcription	Thymus	Thymus
24	chr7:38249600-38256400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:38249800-38256000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:38251200-38261400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:38251400-38256400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:38251400-38256400	Weak transcription	Left Ventricle	heart
29	chr7:38251600-38255400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:38251600-38255600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:38251600-38270400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:38251800-38256200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:38251800-38256200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:38251800-38270200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr7:38252000-38272400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:38252000-38273000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:38252400-38256000	Weak transcription	Right Atrium	heart
38	chr7:38252400-38256000	Weak transcription	Right Ventricle	heart
39	chr7:38253000-38255400	Weak transcription	Primary T cells from cord blood	blood
40	chr7:38253400-38255600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:38253400-38256600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:38253600-38255400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr7:38253600-38256400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr7:38253600-38256400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:38253600-38256400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:38253800-38255600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:38253800-38256400	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr7:38253800-38267400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr7:38254000-38255600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:38254000-38256200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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