Variant report

Variant	rs61852641
Chromosome Location	chr1:247239556-247239557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247239136..247240695-chr1:247358681..247361608,2	K562	blood:
2	chr1:247239357..247243782-chr1:247265039..247269405,6	MCF-7	breast:
3	chr1:247236891..247239039-chr1:247239460..247241318,2	MCF-7	breast:
4	chr1:247237656..247243483-chr1:247491762..247497969,8	K562	blood:
5	chr1:247229715..247234769-chr1:247235903..247241738,8	K562	blood:
6	chr1:247236513..247243563-chr1:247264600..247268970,10	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction
ENSG00000188295	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10802462	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802467	0.94[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]
rs10924899	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112137	1.00[ASN][1000 genomes]
rs12060791	1.00[ASN][1000 genomes]
rs12116484	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118487	1.00[ASN][1000 genomes]
rs12120876	0.91[EUR][1000 genomes]
rs12122044	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122047	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122290	1.00[ASN][1000 genomes]
rs12123948	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130075	1.00[ASN][1000 genomes]
rs12131419	1.00[ASN][1000 genomes]
rs12135842	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135986	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139893	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141232	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141355	1.00[ASN][1000 genomes]
rs12142305	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144260	1.00[ASN][1000 genomes]
rs1565897	1.00[ASN][1000 genomes]
rs1573897	1.00[ASN][1000 genomes]
rs2055191	1.00[ASN][1000 genomes]
rs2055192	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172973	1.00[ASN][1000 genomes]
rs2380113	1.00[ASN][1000 genomes]
rs28540229	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28614003	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310567	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319379	1.00[ASN][1000 genomes]
rs4634944	1.00[ASN][1000 genomes]
rs4925540	1.00[ASN][1000 genomes]
rs4925622	1.00[ASN][1000 genomes]
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	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61498462	1.00[ASN][1000 genomes]
rs61852608	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61852610	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852625	0.85[EUR][1000 genomes]
rs61852630	1.00[ASN][1000 genomes]
rs61852637	1.00[ASN][1000 genomes]
rs61852638	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852639	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852640	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852642	1.00[ASN][1000 genomes]
rs61852646	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426214	1.00[ASN][1000 genomes]
rs6426216	1.00[ASN][1000 genomes]
rs6657686	1.00[ASN][1000 genomes]
rs6663359	0.90[EUR][1000 genomes]
rs6664217	1.00[ASN][1000 genomes]
rs6666242	0.94[EUR][1000 genomes]
rs6681667	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6689229	1.00[ASN][1000 genomes]
rs6701582	1.00[ASN][1000 genomes]
rs6701955	0.94[EUR][1000 genomes]
rs71566692	0.92[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	0.85[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	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542852	1.00[ASN][1000 genomes]
rs7543803	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546342	1.00[ASN][1000 genomes]
rs7546777	1.00[ASN][1000 genomes]
rs7547915	1.00[ASN][1000 genomes]
rs7549105	1.00[ASN][1000 genomes]
rs7549410	1.00[ASN][1000 genomes]
rs7549531	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550095	0.89[EUR][1000 genomes]
rs7551896	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	nsv873428	chr1:247226986-247346189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	nsv873429	chr1:247230809-247288469	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
25	nsv549547	chr1:247233156-247281769	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
26	nsv873430	chr1:247233156-247291400	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247218600-247240600	Weak transcription	HSMMtube	muscle
2	chr1:247219000-247240400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:247219600-247240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:247227600-247241400	Weak transcription	Pancreas	Pancrea
5	chr1:247227800-247241000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:247227800-247241000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:247228000-247241000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:247228200-247240400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:247231800-247240600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:247235200-247240600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:247235800-247241000	Weak transcription	HSMM	muscle
12	chr1:247236000-247240400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:247236000-247240400	Weak transcription	NHLF	lung
14	chr1:247236200-247239600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr1:247236200-247239600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:247236400-247241000	Weak transcription	Fetal Intestine Large	intestine
17	chr1:247236600-247239600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:247236600-247240400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
19	chr1:247236800-247240800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:247236800-247240800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:247236800-247241000	Weak transcription	Fetal Lung	lung
22	chr1:247236800-247241000	Weak transcription	Ovary	ovary
23	chr1:247237000-247239600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:247237200-247240600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:247237200-247241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:247237200-247241000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:247237400-247241000	Weak transcription	Stomach Mucosa	stomach
28	chr1:247237800-247239600	ZNF genes & repeats	Dnd41	blood
29	chr1:247237800-247240600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:247237800-247240800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:247237800-247240800	Weak transcription	A549	lung
32	chr1:247238000-247241000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:247238200-247240600	Weak transcription	Small Intestine	intestine
34	chr1:247238200-247240600	Weak transcription	HUVEC	blood vessel
35	chr1:247238200-247241000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:247238200-247241000	Weak transcription	Fetal Stomach	stomach
37	chr1:247238400-247240200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:247238400-247240400	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:247238400-247240400	Weak transcription	Thymus	Thymus
40	chr1:247238400-247240600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:247238400-247240600	Weak transcription	Fetal Brain Male	brain
42	chr1:247238400-247240600	Weak transcription	K562	blood
43	chr1:247238400-247241400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:247238600-247240400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:247238600-247240800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:247238800-247240200	Weak transcription	Hela-S3	cervix
47	chr1:247239000-247240200	Active TSS	HepG2	liver
48	chr1:247239000-247240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:247239000-247240800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:247239000-247240800	Weak transcription	Monocytes-CD14+_RO01746	blood

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