Variant report

Variant	rs61953541
Chromosome Location	chr12:124013099-124013100
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124008463..124013124-chr12:124014349..124019990,8	MCF-7	breast:
2	chr12:124007811..124010230-chr12:124011879..124014265,2	MCF-7	breast:
3	chr12:124011402..124015187-chr12:124015616..124018872,7	K562	blood:
4	chr12:124008800..124013373-chr12:124015066..124019267,4	K562	blood:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13302918	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1533246	0.80[EUR][1000 genomes]
rs28492040	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28604461	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647680	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28833471	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34734800	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930704	0.83[ASN][1000 genomes]
rs4930717	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953540	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488877	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7313751	0.83[ASN][1000 genomes]
rs7398935	0.83[ASN][1000 genomes]
rs7956299	0.83[ASN][1000 genomes]
rs7962151	0.83[ASN][1000 genomes]
rs7963804	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv560495	chr12:124012974-124017461	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:123994400-124016200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:123994600-124016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:123995200-124016400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:123999200-124015800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:123999400-124016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:124000600-124015000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:124001000-124016400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:124001200-124017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:124001400-124017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:124002000-124016800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:124003000-124015400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:124004600-124016800	Weak transcription	Stomach Mucosa	stomach
14	chr12:124004800-124014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:124004800-124016600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:124005600-124015200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:124005600-124016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:124005600-124016400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:124005600-124016400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:124005800-124015800	Weak transcription	NHDF-Ad	bronchial
21	chr12:124005800-124016400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:124005800-124016600	Weak transcription	Fetal Kidney	kidney
23	chr12:124006000-124015000	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:124006000-124015400	Weak transcription	Fetal Brain Male	brain
25	chr12:124006200-124017600	Weak transcription	Small Intestine	intestine
26	chr12:124006800-124016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:124007200-124016600	Weak transcription	Primary T cells from cord blood	blood
28	chr12:124007800-124015200	Weak transcription	HUVEC	blood vessel
29	chr12:124007800-124016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:124007800-124016600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:124007800-124017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:124007800-124017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:124008000-124014400	Weak transcription	HSMM	muscle
34	chr12:124008000-124015400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:124008000-124016000	Weak transcription	Hela-S3	cervix
36	chr12:124008000-124016400	Weak transcription	Dnd41	blood
37	chr12:124008000-124017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:124008000-124017400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:124008200-124014200	Weak transcription	NHLF	lung
40	chr12:124008200-124015200	Weak transcription	Pancreas	Pancrea
41	chr12:124008200-124016600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:124008200-124017200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:124008400-124016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:124008400-124017400	Weak transcription	Gastric	stomach
45	chr12:124008600-124015200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:124008800-124015200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:124009000-124013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:124009000-124013400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:124009000-124015000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:124009000-124015400	Weak transcription	Brain Germinal Matrix	brain

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