Variant report

Variant	rs3761278
Chromosome Location	chr20:23329871-23329872
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23329648-23333051	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:23329714-23332919	IMR90	lung:	n/a	n/a
3	MYC	chr20:23329608-23332518	A549	lung:	n/a	chr20:23331798-23331809 chr20:23330889-23330905 chr20:23331800-23331809 chr20:23331798-23331808 chr20:23330889-23330896 chr20:23331797-23331812 chr20:23330744-23330753 chr20:23330734-23330744 chr20:23330887-23330896 chr20:23331797-23331810 chr20:23331799-23331809
4	MXI1	chr20:23329728-23332953	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr20:23329826-23330119	GM12878	blood:	n/a	n/a
6	CTCF	chr20:23329801-23331682	SK-N-SH	brain:	n/a	chr20:23330477-23330493 chr20:23330478-23330499 chr20:23330479-23330492 chr20:23330476-23330494
7	MXI1	chr20:23329824-23333171	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23187473..23190139-chr20:23328538..23331366,2	MCF-7	breast:
2	chr20:23328647..23330996-chr20:23399236..23401652,2	K562	blood:
3	chr20:23321273..23323325-chr20:23328933..23330875,2	K562	blood:
4	chr20:23022684..23024263-chr20:23328966..23331361,2	MCF-7	breast:
5	chr20:23112159..23115128-chr20:23328465..23330957,2	K562	blood:
6	chr20:23325694..23327438-chr20:23329149..23330658,2	MCF-7	breast:

Variant related genes	Relation type
NXT1	TF binding region
ENSG00000233746	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10485644	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1109557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1122407	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs1157263	1.00[CEU][hapmap]
rs12625187	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12625257	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12625297	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs12625468	0.82[AMR][1000 genomes]
rs12625489	1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12625948	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12625994	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs16985266	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs16985303	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16985337	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs2236024	1.00[CEU][hapmap]
rs2983624	1.00[CEU][hapmap]
rs2983645	1.00[CEU][hapmap]
rs3004122	1.00[CEU][hapmap]
rs34036626	0.94[AMR][1000 genomes]
rs34831633	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736756	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes]
rs3761276	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56693860	0.82[AMR][1000 genomes]
rs57034369	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57322153	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57436024	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57535381	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58192622	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59143301	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6048853	1.00[CEU][hapmap]
rs6048856	1.00[CEU][hapmap]
rs60799291	0.89[AMR][1000 genomes]
rs6083140	1.00[CEU][hapmap]
rs61024391	1.00[AMR][1000 genomes]
rs6114159	1.00[CEU][hapmap]
rs6114160	1.00[CEU][hapmap]
rs6114167	1.00[CEU][hapmap]
rs61297472	0.89[AMR][1000 genomes]
rs61344818	0.94[AMR][1000 genomes]
rs7265627	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7266535	1.00[CEU][hapmap]
rs73901826	0.82[AMR][1000 genomes]
rs73901859	1.00[AMR][1000 genomes]
rs8115832	1.00[AMR][1000 genomes]
rs8117246	0.82[AMR][1000 genomes]
rs8123389	0.95[AMR][1000 genomes]
rs8125332	0.82[AMR][1000 genomes]

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23326200-23330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:23327000-23330400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23327000-23330800	Weak transcription	Spleen	Spleen
4	chr20:23327200-23330000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:23327400-23330000	Weak transcription	HSMM	muscle
6	chr20:23327600-23330000	Weak transcription	Pancreas	Pancrea
7	chr20:23328000-23330000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr20:23328200-23330000	Weak transcription	Adipose Nuclei	Adipose
9	chr20:23328600-23330000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr20:23328800-23330000	Weak transcription	Fetal Kidney	kidney
11	chr20:23329000-23330000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr20:23329000-23330000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr20:23329000-23330000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr20:23329000-23330000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr20:23329000-23330000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr20:23329000-23330200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:23329400-23330000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:23329400-23330000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:23329400-23330000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:23329400-23330000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:23329400-23330000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr20:23329400-23330000	Enhancers	Fetal Intestine Large	intestine
23	chr20:23329400-23330000	Enhancers	Fetal Intestine Small	intestine
24	chr20:23329400-23330000	Enhancers	Fetal Stomach	stomach
25	chr20:23329400-23330000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr20:23329400-23330000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr20:23329400-23330200	Enhancers	Fetal Muscle Leg	muscle
28	chr20:23329400-23330200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr20:23329400-23330400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr20:23329400-23330400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr20:23329400-23330400	Enhancers	Placenta	Placenta
32	chr20:23329400-23330600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr20:23329600-23330000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr20:23329600-23330000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:23329600-23330000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr20:23329600-23330000	Enhancers	Primary T cells from cord blood	blood
37	chr20:23329600-23330000	Enhancers	Primary hematopoietic stem cells	blood
38	chr20:23329600-23330000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr20:23329600-23330000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr20:23329600-23330000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:23329600-23330000	Enhancers	Liver	Liver
42	chr20:23329600-23330000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr20:23329600-23330000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr20:23329600-23330000	Flanking Active TSS	HepG2	liver
45	chr20:23329600-23330000	Enhancers	HSMMtube	muscle
46	chr20:23329600-23330000	Enhancers	NHDF-Ad	bronchial
47	chr20:23329600-23330000	Enhancers	NHLF	lung
48	chr20:23329600-23330200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr20:23329600-23330200	Enhancers	Primary B cells from cord blood	blood
50	chr20:23329600-23330200	Enhancers	Primary B cells from peripheral blood	blood

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