Variant report

Variant	rs10924899
Chromosome Location	chr1:247226344-247226345
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	chr1:247225416..247227958-chr1:247241143..247243199,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135747	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10802462	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802467	0.88[EUR][1000 genomes]
rs10924892	1.00[ASN][1000 genomes]
rs10924895	1.00[ASN][1000 genomes]
rs10924896	1.00[ASN][1000 genomes]
rs10924897	1.00[ASN][1000 genomes]
rs1112137	1.00[ASN][1000 genomes]
rs12060791	1.00[ASN][1000 genomes]
rs12116484	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118487	1.00[ASN][1000 genomes]
rs12120876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12122044	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122047	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122290	1.00[ASN][1000 genomes]
rs12123948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130075	1.00[ASN][1000 genomes]
rs12131419	1.00[ASN][1000 genomes]
rs12135374	1.00[CHD][hapmap]
rs12135842	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135986	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139893	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141232	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141355	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12142305	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144260	1.00[ASN][1000 genomes]
rs12563431	0.91[CEU][hapmap]
rs1565897	1.00[ASN][1000 genomes]
rs1573897	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2055191	1.00[ASN][1000 genomes]
rs2055192	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172973	1.00[ASN][1000 genomes]
rs2379189	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs2380113	1.00[ASN][1000 genomes]
rs2642956	1.00[CHD][hapmap]
rs2642978	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs28540229	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28614003	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319379	1.00[ASN][1000 genomes]
rs4634944	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4925540	1.00[ASN][1000 genomes]
rs4925622	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4925700	1.00[CHD][hapmap]
rs4971315	1.00[ASN][1000 genomes]
rs4971316	1.00[ASN][1000 genomes]
rs4971317	1.00[ASN][1000 genomes]
rs4971319	1.00[ASN][1000 genomes]
rs55984722	1.00[ASN][1000 genomes]
rs56884994	1.00[ASN][1000 genomes]
rs59525684	1.00[ASN][1000 genomes]
rs61373194	1.00[ASN][1000 genomes]
rs61498462	1.00[ASN][1000 genomes]
rs61852608	1.00[ASN][1000 genomes]
rs61852610	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852625	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61852630	1.00[ASN][1000 genomes]
rs61852637	1.00[ASN][1000 genomes]
rs61852638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852639	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852640	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852641	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852642	1.00[ASN][1000 genomes]
rs61852646	0.84[EUR][1000 genomes]
rs6426214	1.00[ASN][1000 genomes]
rs6426216	1.00[ASN][1000 genomes]
rs6657686	1.00[ASN][1000 genomes]
rs6663359	0.84[EUR][1000 genomes]
rs6663885	0.87[AFR][1000 genomes]
rs6664217	1.00[ASN][1000 genomes]
rs6666242	0.88[EUR][1000 genomes]
rs6681667	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6689229	1.00[ASN][1000 genomes]
rs6698643	1.00[CHD][hapmap]
rs6701582	1.00[ASN][1000 genomes]
rs6701955	0.88[EUR][1000 genomes]
rs71566692	0.86[EUR][1000 genomes]
rs72768397	1.00[ASN][1000 genomes]
rs7418825	1.00[ASN][1000 genomes]
rs7511962	1.00[ASN][1000 genomes]
rs7512099	1.00[ASN][1000 genomes]
rs7512150	1.00[ASN][1000 genomes]
rs7513678	1.00[ASN][1000 genomes]
rs7518427	1.00[ASN][1000 genomes]
rs7519795	1.00[ASN][1000 genomes]
rs7521422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522300	1.00[ASN][1000 genomes]
rs7526191	1.00[ASN][1000 genomes]
rs7535251	1.00[ASN][1000 genomes]
rs7535264	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542852	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7543803	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546342	1.00[ASN][1000 genomes]
rs7546777	1.00[ASN][1000 genomes]
rs7547915	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7549105	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7549410	1.00[ASN][1000 genomes]
rs7549531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550095	1.00[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7551896	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553547	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
11	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
12	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
13	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
14	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
15	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
16	nsv999352	chr1:247180668-247307074	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv535421	chr1:247180668-247307074	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
22	nsv533111	chr1:247200511-247264759	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1014012	chr1:247207932-247289138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10924899	ZNF669	cis	cerebellum	SCAN
rs10924899	ZNF669	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247218600-247240600	Weak transcription	HSMMtube	muscle
2	chr1:247218800-247227200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:247218800-247227200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:247219000-247240400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:247219600-247240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:247221000-247227000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:247223200-247230400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:247224800-247229600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr1:247225600-247226600	ZNF genes & repeats	Primary T cells from cord blood	blood
10	chr1:247225800-247227600	ZNF genes & repeats	Fetal Stomach	stomach
11	chr1:247225800-247228400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:247225800-247228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:247225800-247229800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:247226000-247226600	Enhancers	HepG2	liver
15	chr1:247226000-247227000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:247226000-247227000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:247226000-247227200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:247226000-247228000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr1:247226000-247229800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr1:247226200-247232000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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