Variant report

Variant	rs12892062
Chromosome Location	chr14:103883512-103883513
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	EBF1	chr14:103883299-103883674	GM12878	blood:	n/a	chr14:103883540-103883551
2	EP300	chr14:103883456-103883698	GM12878	blood:	n/a	n/a
3	MAX	chr14:103883453-103883660	H1-hESC	embryonic stem cell:	n/a	n/a
4	EBF1	chr14:103883330-103883724	GM12878	blood:	n/a	chr14:103883540-103883551

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:103876768..103879568-chr14:103882112..103883749,2	MCF-7	breast:
2	chr14:103799657..103801289-chr14:103882797..103884617,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244691	TF binding region
MARK3	TF binding region
ENSG00000244691	Chromatin interaction
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10459573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11160750	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11541718	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11625172	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12147655	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12185021	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12588705	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12879663	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12881583	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12882130	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs12883668	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12885234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12885714	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12885762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12885786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12888042	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12889703	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12894275	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12896612	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12896832	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12896919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17617094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17617307	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17617832	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17617935	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17679729	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17680085	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1951389	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2065015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2065016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2065017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2065018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236281	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2246490	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2296487	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2756138	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28711288	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34161327	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34347076	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34372508	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34479426	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34606394	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35056010	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35126287	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35224956	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35339837	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35344594	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35366629	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35443927	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35466180	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35771849	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35799018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35862113	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35999760	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3783396	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783397	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783398	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3783400	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4900574	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4900575	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4906323	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4906327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4906330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4906331	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4906332	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55731474	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55930273	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59858038	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7141674	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71417863	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7143609	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7155822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7155980	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7159665	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7161305	0.83[JPT][hapmap]
rs7401563	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8004501	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8004780	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8012127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8012623	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911549	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
2	chr14:103868400-103883800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:103871000-103883600	Strong transcription	Dnd41	blood
4	chr14:103871000-103884400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:103872200-103883800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr14:103874600-103884200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:103874600-103900800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:103875200-103888200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:103875200-103889200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:103875200-103893600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr14:103875400-103883600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:103875400-103884200	Weak transcription	Psoas Muscle	Psoas
13	chr14:103875400-103884600	Weak transcription	Small Intestine	intestine
14	chr14:103875400-103887400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr14:103875400-103888600	Weak transcription	Gastric	stomach
16	chr14:103875400-103889600	Weak transcription	Colon Smooth Muscle	Colon
17	chr14:103875400-103892200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr14:103875400-103893600	Weak transcription	Brain Germinal Matrix	brain
19	chr14:103875600-103884600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr14:103875600-103893800	Weak transcription	Fetal Heart	heart
21	chr14:103875600-103894000	Weak transcription	Fetal Brain Male	brain
22	chr14:103875800-103889800	Weak transcription	Lung	lung
23	chr14:103876800-103887800	Weak transcription	Pancreas	Pancrea
24	chr14:103879000-103883800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr14:103879000-103892800	Weak transcription	Spleen	Spleen
26	chr14:103879000-103895200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr14:103879000-103914200	Weak transcription	Esophagus	oesophagus
28	chr14:103879000-103941400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:103879200-103887200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr14:103879600-103889400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr14:103879800-103887400	Weak transcription	HepG2	liver
32	chr14:103880200-103884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:103880400-103894200	Weak transcription	Liver	Liver
34	chr14:103880400-103904600	Weak transcription	Fetal Kidney	kidney
35	chr14:103881000-103883800	Weak transcription	Primary T cells from cord blood	blood
36	chr14:103881000-103887000	Weak transcription	Thymus	Thymus
37	chr14:103881000-103889200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr14:103881000-103890600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr14:103881000-103900600	Weak transcription	Placenta	Placenta
40	chr14:103881200-103883800	Weak transcription	HUVEC	blood vessel
41	chr14:103882000-103883600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr14:103882000-103884000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr14:103882000-103886000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr14:103882000-103887200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr14:103882200-103883600	Strong transcription	HMEC	breast
46	chr14:103882200-103884600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr14:103882400-103883600	Strong transcription	Fetal Stomach	stomach
48	chr14:103882400-103883800	Weak transcription	Primary B cells from cord blood	blood
49	chr14:103882600-103883600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr14:103882600-103883600	Strong transcription	Rectal Mucosa Donor 31	rectum

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