Variant report

Variant	rs12110161
Chromosome Location	chr5:14397728-14397729
allele	A/G
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	JUND	chr5:14397332-14402457	SK-N-SH	brain:	n/a	chr5:14398493-14398507 chr5:14400452-14400461 chr5:14398516-14398530 chr5:14399615-14399622
2	POLR2A	chr5:14397648-14398245	SK-N-SH	brain:	n/a	n/a
3	CEBPB	chr5:14397582-14397772	Hela-S3	cervix:	n/a	chr5:14397633-14397650 chr5:14397636-14397649 chr5:14397636-14397647
4	NFIC	chr5:14397700-14398346	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr5:14397627-14398441	SK-N-SH	brain:	n/a	n/a
6	EP300	chr5:14397725-14398444	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr5:14397364-14398373	PANC-1	pancreas:	n/a	n/a
8	TCF12	chr5:14397661-14398466	SK-N-SH	brain:	n/a	n/a
9	STAT3	chr5:14397698-14397741	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:14397557-14398721	U87	brain:	n/a	n/a
11	TCF12	chr5:14397674-14398497	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14386511..14389114-chr5:14396978..14399315,3	MCF-7	breast:

Variant related genes	Relation type
TRIO	TF binding region
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10866506	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10866507	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11949756	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11950000	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11959397	0.89[EUR][1000 genomes]
rs12109453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109756	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109880	0.89[EUR][1000 genomes]
rs12110267	0.89[EUR][1000 genomes]
rs16903421	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16903423	0.89[EUR][1000 genomes]
rs16903428	0.89[EUR][1000 genomes]
rs16903434	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16903453	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903460	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903464	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903497	0.95[YRI][hapmap]
rs2463803	0.85[CEU][hapmap]
rs35373258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56689214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57017859	0.89[EUR][1000 genomes]
rs57640930	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59405120	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60738268	0.89[EUR][1000 genomes]
rs60892841	0.93[EUR][1000 genomes]
rs61059406	0.89[EUR][1000 genomes]
rs61469842	0.84[EUR][1000 genomes]
rs62344979	0.89[EUR][1000 genomes]
rs62344981	0.86[EUR][1000 genomes]
rs62344983	0.89[EUR][1000 genomes]
rs62345009	0.84[EUR][1000 genomes]
rs62345012	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62345015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66554336	0.89[EUR][1000 genomes]
rs6883134	0.95[YRI][hapmap]
rs697559	0.82[CEU][hapmap]
rs73061636	0.91[EUR][1000 genomes]
rs7706484	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7715916	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs773764	0.82[CEU][hapmap]
rs773765	0.82[CEU][hapmap]
rs773766	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr5:14354600-14402400	Strong transcription	Liver	Liver
4	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
6	chr5:14360000-14398400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:14366800-14403200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:14367400-14399800	Strong transcription	Left Ventricle	heart
11	chr5:14372400-14398600	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:14374400-14399600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:14380400-14402800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr5:14385600-14399000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:14386400-14399600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:14386800-14398600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:14387200-14397800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:14387200-14398600	Strong transcription	A549	lung
19	chr5:14387200-14405800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:14387800-14399800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:14388000-14399600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:14388000-14402200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:14388200-14398000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:14388200-14400200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:14388600-14398000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:14388600-14399600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:14388600-14402600	Strong transcription	Fetal Intestine Large	intestine
28	chr5:14388800-14407200	Weak transcription	Small Intestine	intestine
29	chr5:14389000-14398000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:14390600-14399800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:14392000-14399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:14392200-14402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:14392200-14406600	Weak transcription	Primary T cells from cord blood	blood
34	chr5:14392400-14398600	Strong transcription	Fetal Muscle Leg	muscle
35	chr5:14392400-14399600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:14392400-14399600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:14392400-14399600	Weak transcription	Fetal Brain Male	brain
38	chr5:14392400-14406000	Weak transcription	Fetal Heart	heart
39	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
40	chr5:14392600-14403600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:14392800-14397800	Strong transcription	Fetal Stomach	stomach
42	chr5:14393200-14398400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr5:14393200-14402800	Strong transcription	Placenta	Placenta
44	chr5:14393400-14398200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:14393400-14402400	Strong transcription	GM12878-XiMat	blood
46	chr5:14393400-14403200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:14393600-14398000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:14393600-14398000	Strong transcription	Brain Germinal Matrix	brain
49	chr5:14393600-14398600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:14393600-14413600	Strong transcription	Primary B cells from cord blood	blood

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