Variant report

Variant	rs176941
Chromosome Location	chr14:78175326-78175327
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:78173960-78175334	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:78173770-78175937	GM12878	blood:	n/a	n/a
3	SREBP1	chr14:78173414-78177367	GM12878	blood:	n/a	n/a
4	SIN3A	chr14:78173486-78175850	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD1	chr14:78173476-78175605	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr14:78172988-78176324	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr14:78173461-78175360	GM12878	blood:	n/a	n/a
8	POLR2A	chr14:78175254-78175957	MCF10A-Er-Src	breast:	n/a	n/a
9	IRF1	chr14:78175311-78175949	K562	blood:	n/a	n/a
10	POLR2A	chr14:78173574-78176008	GM12891	blood:	n/a	n/a
11	STAT3	chr14:78174436-78175487	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr14:78173657-78175796	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr14:78173411-78175391	IMR90	lung:	n/a	n/a
14	SIN3AK20	chr14:78173382-78175350	MCF-7	breast:	n/a	n/a
15	POLR2A	chr14:78173817-78175523	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:77934304..77936307-chr14:78175272..78177718,2	K562	blood:
2	chr14:77922378..77925268-chr14:78174504..78177181,3	MCF-7	breast:
3	chr14:78173677..78176352-chr14:78201271..78203886,2	MCF-7	breast:
4	chr14:78174606..78176919-chr14:78226054..78227853,2	MCF-7	breast:
5	chr14:77772512..77775137-chr14:78173113..78175507,2	MCF-7	breast:
6	chr14:78173879..78175943-chr14:78227117..78229069,2	K562	blood:
7	chr14:78173055..78176036-chr8:144819518..144822439,2	MCF-7	breast:
8	chr14:78169975..78173523-chr14:78173651..78176580,3	MCF-7	breast:
9	chr14:78116603..78122891-chr14:78172785..78176058,7	MCF-7	breast:
10	chr14:78173969..78175847-chr14:78226797..78229509,2	MCF-7	breast:
11	chr14:78013590..78016333-chr14:78173040..78175809,2	MCF-7	breast:
12	chr14:78166641..78172350-chr14:78172652..78176323,11	MCF-7	breast:

No data

Variant related genes	Relation type
ALKBH1	TF binding region
SLIRP	TF binding region
ENSG00000240233	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000151445	Chromatin interaction
ENSG00000100591	Chromatin interaction
ENSG00000100601	Chromatin interaction
ENSG00000268208	Chromatin interaction
ENSG00000100603	Chromatin interaction
ENSG00000258668	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000197734	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1006038	0.90[CHB][hapmap]
rs1006039	0.90[CHB][hapmap]
rs1006040	0.90[CHB][hapmap]
rs1008988	0.95[CHB][hapmap]
rs10134425	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10138747	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10139492	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10142722	0.90[CHB][hapmap]
rs10143249	0.90[ASN][1000 genomes]
rs10143294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10144448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10146255	0.90[ASN][1000 genomes]
rs1048147	0.90[CHB][hapmap]
rs10483885	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs114763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11621719	0.87[ASN][1000 genomes]
rs11622761	0.87[ASN][1000 genomes]
rs11624118	0.86[ASN][1000 genomes]
rs11628888	0.85[CHB][hapmap]
rs11846215	0.83[ASN][1000 genomes]
rs12879880	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12885306	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs12887313	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12890728	0.85[CHB][hapmap]
rs12890828	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1477262	0.90[CHB][hapmap]
rs1477263	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477264	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17106157	0.90[CHB][hapmap]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176947	0.95[ASN][1000 genomes]
rs176948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176951	0.90[CHB][hapmap]
rs176954	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176961	0.98[ASN][1000 genomes]
rs176963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176964	0.90[CHB][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176968	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176969	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176970	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176972	0.98[ASN][1000 genomes]
rs176975	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176976	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176977	0.95[ASN][1000 genomes]
rs176980	0.90[CHB][hapmap]
rs2080703	0.93[ASN][1000 genomes]
rs2111831	0.83[ASN][1000 genomes]
rs2267756	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2267759	0.90[CHB][hapmap]
rs2267760	0.90[CHB][hapmap]
rs2267761	0.90[CHB][hapmap]
rs2267762	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267763	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2267764	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2267766	0.89[AMR][1000 genomes]
rs2277917	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2284233	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299930	0.90[CHB][hapmap]
rs3759728	0.90[CHB][hapmap]
rs3783980	0.90[CHB][hapmap]
rs3783981	0.93[ASN][1000 genomes]
rs3783982	0.93[ASN][1000 genomes]
rs4632066	0.90[CHB][hapmap]
rs4641655	0.90[ASN][1000 genomes]
rs4899670	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4899673	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4899674	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4903638	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61992864	0.82[ASN][1000 genomes]
rs61992867	0.84[ASN][1000 genomes]
rs61992868	0.84[ASN][1000 genomes]
rs6574392	0.95[ASN][1000 genomes]
rs6574394	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6574404	0.86[CHB][hapmap]
rs7142390	0.90[CHB][hapmap]
rs7143926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145717	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7148078	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7148126	0.93[ASN][1000 genomes]
rs7150531	0.88[ASN][1000 genomes]
rs7151685	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7154571	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7159310	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7160355	0.94[ASN][1000 genomes]
rs717682	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72210300	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs759713	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8003691	0.90[CHB][hapmap]
rs8010541	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8016447	0.90[CHB][hapmap]
rs8022516	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9323649	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9323650	0.90[CHB][hapmap]
rs9323651	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs176941	RPS6KL1	cis	cerebellum	SCAN
rs176941	ALDH6A1	cis	parietal	SCAN
rs176941	NEK9	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78172600-78175800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr14:78172600-78176000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr14:78172800-78175800	Active TSS	A549	lung
4	chr14:78172800-78176400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr14:78172800-78176400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:78172800-78176600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr14:78173000-78175600	Active TSS	Psoas Muscle	Psoas
8	chr14:78173000-78175800	Active TSS	Right Atrium	heart
9	chr14:78173000-78176200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:78173200-78175400	Active TSS	Fetal Muscle Trunk	muscle
11	chr14:78173200-78175600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:78173200-78175600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr14:78173200-78175600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr14:78173200-78175600	Active TSS	Muscle Satellite Cultured Cells	--
15	chr14:78173200-78176000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr14:78173200-78176000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr14:78173200-78176200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:78173200-78176200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr14:78173400-78175400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr14:78173400-78175400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr14:78173400-78175400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr14:78173400-78175400	Active TSS	Fetal Kidney	kidney
23	chr14:78173400-78175400	Active TSS	Gastric	stomach
24	chr14:78173400-78175400	Active TSS	Small Intestine	intestine
25	chr14:78173400-78175400	Active TSS	Hela-S3	cervix
26	chr14:78173400-78175400	Active TSS	HSMM	muscle
27	chr14:78173400-78175600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr14:78173400-78175600	Active TSS	Aorta	Aorta
29	chr14:78173400-78175600	Active TSS	HSMMtube	muscle
30	chr14:78173400-78175600	Active TSS	K562	blood
31	chr14:78173400-78175600	Active TSS	NHDF-Ad	bronchial
32	chr14:78173400-78175800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:78173400-78175800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr14:78173400-78175800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr14:78173400-78175800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr14:78173400-78175800	Active TSS	Right Ventricle	heart
37	chr14:78173400-78175800	Active TSS	GM12878-XiMat	blood
38	chr14:78173400-78175800	Bivalent/Poised TSS	HepG2	liver
39	chr14:78173400-78175800	Active TSS	NHLF	lung
40	chr14:78173400-78176400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr14:78173400-78176800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr14:78173600-78175400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr14:78173600-78175400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr14:78173600-78175400	Active TSS	Left Ventricle	heart
45	chr14:78173600-78175400	Active TSS	Lung	lung
46	chr14:78173600-78175400	Active TSS	Pancreas	Pancrea
47	chr14:78173600-78175400	Active TSS	NH-A	brain
48	chr14:78173600-78175400	Active TSS	NHEK	skin
49	chr14:78173600-78175600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:78173600-78175600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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