Variant report

Variant	rs2642973
Chromosome Location	chr1:247162658-247162659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247162509..247164222-chr1:247168923..247171107,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AHCTF1-3	chr1:247162650-247162742	NR_037894
2	lnc-AHCTF1-3	chr1:247162650-247162742	NR_037892

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1018048	1.00[ASN][1000 genomes]
rs10737797	1.00[ASN][1000 genomes]
rs10754535	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10802455	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10802456	0.92[ASN][1000 genomes]
rs10802457	1.00[JPT][hapmap]
rs10802458	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10802460	1.00[ASN][1000 genomes]
rs10802461	1.00[ASN][1000 genomes]
rs10924879	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12030877	0.85[ASN][1000 genomes]
rs12045053	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12048616	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12057312	0.92[ASN][1000 genomes]
rs12119510	1.00[JPT][hapmap]
rs12405787	1.00[ASN][1000 genomes]
rs12563635	1.00[ASN][1000 genomes]
rs1546143	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1691228	1.00[JPT][hapmap]
rs1874200	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2379189	0.80[YRI][hapmap]
rs2453405	1.00[ASN][1000 genomes]
rs2453407	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2642992	0.92[ASN][1000 genomes]
rs2642993	1.00[JPT][hapmap]
rs2642995	0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2818876	0.92[ASN][1000 genomes]
rs3104110	0.92[ASN][1000 genomes]
rs3749427	0.92[ASN][1000 genomes]
rs4384270	1.00[JPT][hapmap]
rs4506496	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4971301	0.92[ASN][1000 genomes]
rs4971306	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4971310	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs61852611	0.92[ASN][1000 genomes]
rs6426194	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6668864	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6678796	1.00[ASN][1000 genomes]
rs6694946	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6698318	1.00[ASN][1000 genomes]
rs6702728	1.00[ASN][1000 genomes]
rs7513728	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7516037	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7519943	0.84[ASN][1000 genomes]
rs7544897	1.00[ASN][1000 genomes]
rs7555643	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv524007	chr1:247098587-247162658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
13	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
14	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv549546	chr1:247145690-247205056	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2642973	ZNF669	cis	parietal	SCAN
rs2642973	C1orf150	cis	cerebellum	SCAN
rs2642973	ZNF669	cis	cerebellum	SCAN
rs2642973	C1orf100	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247136600-247164600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:247140600-247163400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:247140800-247162800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr1:247144200-247163600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:247151200-247170800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:247151600-247170000	Weak transcription	Osteobl	bone
7	chr1:247155200-247168800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:247155800-247163200	ZNF genes & repeats	Fetal Brain Female	brain
9	chr1:247156200-247163400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:247156400-247163200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:247158000-247170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:247158200-247163400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr1:247158400-247163200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:247158400-247163600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr1:247158400-247164400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:247158400-247167800	Weak transcription	HUVEC	blood vessel
17	chr1:247158600-247163400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr1:247158600-247164200	Weak transcription	Small Intestine	intestine
19	chr1:247159000-247163400	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr1:247159200-247165800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:247159600-247164200	Weak transcription	HepG2	liver
22	chr1:247159600-247170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:247159800-247163400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:247159800-247163400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:247159800-247166200	Weak transcription	Hela-S3	cervix
26	chr1:247160200-247163400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:247160600-247163000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:247160600-247163400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:247160800-247164600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr1:247161000-247163400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:247161200-247163800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:247161200-247164400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
33	chr1:247161800-247163000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:247161800-247163200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr1:247161800-247163400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:247161800-247163400	Strong transcription	Fetal Thymus	thymus
37	chr1:247161800-247166400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:247162000-247162800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:247162000-247162800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:247162000-247162800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:247162000-247163200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:247162000-247163400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:247162200-247162800	ZNF genes & repeats	Fetal Stomach	stomach
44	chr1:247162200-247163400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
45	chr1:247162200-247163600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:247162400-247162800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
47	chr1:247162400-247162800	ZNF genes & repeats	Fetal Intestine Large	intestine
48	chr1:247162400-247162800	ZNF genes & repeats	Fetal Lung	lung
49	chr1:247162400-247162800	ZNF genes & repeats	HSMM	muscle
50	chr1:247162400-247163400	ZNF genes & repeats	Fetal Brain Male	brain

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