Variant report

Variant	rs2955969
Chromosome Location	chr15:44114527-44114528
allele	C/T
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	ZNF384	chr15:44114248-44114573	GM12878	blood:	n/a	n/a
2	ZNF384	chr15:44114226-44114606	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44089858..44095024-chr15:44113933..44120718,10	MCF-7	breast:
2	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:
3	chr15:44082407..44088245-chr15:44114276..44118984,12	MCF-7	breast:
4	chr15:44112442..44117510-chr15:44119138..44122295,7	K562	blood:

Variant related genes	Relation type
WDR76	TF binding region
ENSG00000092470	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000242028	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10163054	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10438303	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1053492	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11070408	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11070410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070412	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11638972	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11852840	0.90[ASN][1000 genomes]
rs11856495	0.93[ASN][1000 genomes]
rs11856795	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12101756	0.82[ASN][1000 genomes]
rs12440573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12441127	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12441861	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12441984	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12442129	0.86[ASN][1000 genomes]
rs12442297	0.81[CHB][hapmap]
rs12443102	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12908467	0.88[EUR][1000 genomes]
rs13380397	0.86[ASN][1000 genomes]
rs16950562	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16963953	0.94[ASN][1000 genomes]
rs16965120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16977724	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs16977798	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1965794	0.89[ASN][1000 genomes]
rs1965795	0.96[ASN][1000 genomes]
rs1975364	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2228368	0.98[ASN][1000 genomes]
rs2277531	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2411284	0.84[EUR][1000 genomes]
rs2447193	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2447208	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2467402	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2470121	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2788	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs28377539	0.86[ASN][1000 genomes]
rs28413704	0.96[ASN][1000 genomes]
rs28476182	0.95[ASN][1000 genomes]
rs28509275	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs28513374	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs28519630	0.96[ASN][1000 genomes]
rs28524541	0.97[ASN][1000 genomes]
rs28531819	0.97[ASN][1000 genomes]
rs28546844	0.89[ASN][1000 genomes]
rs28564774	0.97[ASN][1000 genomes]
rs28578398	0.91[ASN][1000 genomes]
rs28583806	0.98[ASN][1000 genomes]
rs28590651	1.00[ASN][1000 genomes]
rs28595038	0.83[ASN][1000 genomes]
rs28636829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28674750	0.97[ASN][1000 genomes]
rs28678901	0.93[ASN][1000 genomes]
rs28679673	0.97[ASN][1000 genomes]
rs28684672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28687459	0.97[ASN][1000 genomes]
rs28696802	0.97[ASN][1000 genomes]
rs28707214	0.97[ASN][1000 genomes]
rs28718261	0.83[ASN][1000 genomes]
rs28780699	0.97[ASN][1000 genomes]
rs28781888	0.97[ASN][1000 genomes]
rs28823973	0.88[ASN][1000 genomes]
rs28858500	0.86[ASN][1000 genomes]
rs28866846	0.94[ASN][1000 genomes]
rs28891769	0.91[ASN][1000 genomes]
rs2920781	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2927071	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2927072	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2927085	0.85[CEU][hapmap]
rs3087657	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs35654783	0.81[EUR][1000 genomes]
rs35866764	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3736180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3742982	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3759790	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs3759791	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3816792	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs3825783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3862142	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4332723	0.87[EUR][1000 genomes]
rs4617832	0.84[EUR][1000 genomes]
rs4924720	0.81[EUR][1000 genomes]
rs4924722	0.90[EUR][1000 genomes]
rs4997480	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs524908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs533143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56008017	0.92[ASN][1000 genomes]
rs56909447	0.97[ASN][1000 genomes]
rs575082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60883262	0.92[ASN][1000 genomes]
rs61390361	0.85[ASN][1000 genomes]
rs62018947	0.84[EUR][1000 genomes]
rs62018952	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs663214	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs667476	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs68079546	0.97[ASN][1000 genomes]
rs686666	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs688009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7168158	0.83[ASN][1000 genomes]
rs7169322	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7169382	0.98[ASN][1000 genomes]
rs7169988	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7170167	0.84[ASN][1000 genomes]
rs7170751	0.90[ASN][1000 genomes]
rs7171750	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7174208	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7175032	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7175129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7178343	0.84[EUR][1000 genomes]
rs7179388	0.97[ASN][1000 genomes]
rs7180818	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7181039	0.81[CHB][hapmap]
rs7183809	0.97[ASN][1000 genomes]
rs8023458	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8023508	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs8032649	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs8034451	0.83[EUR][1000 genomes]
rs8040839	0.98[ASN][1000 genomes]
rs8042868	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs9944216	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9989313	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS 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	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2955969	STRCP1	cis	Thyroid	GTEx
rs2955969	AC011330.5	cis	Thyroid	GTEx
rs2955969	AC011330.5	cis	Artery Tibial	GTEx
rs2955969	ZSCAN29	cis	Thyroid	GTEx
rs2955969	STRCP1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44093600-44116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:44093600-44116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44093800-44115800	Weak transcription	Right Atrium	heart
4	chr15:44094000-44114600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:44094000-44114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:44105000-44115800	Weak transcription	Psoas Muscle	Psoas
7	chr15:44106800-44115600	Weak transcription	Right Ventricle	heart
8	chr15:44107200-44116000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:44107400-44115600	Weak transcription	Fetal Heart	heart
10	chr15:44107600-44115400	Weak transcription	Aorta	Aorta
11	chr15:44107800-44115800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:44107800-44115800	Weak transcription	Gastric	stomach
13	chr15:44108000-44115800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:44109400-44115400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:44109800-44114600	Weak transcription	Lung	lung
16	chr15:44109800-44114600	Weak transcription	Ovary	ovary
17	chr15:44109800-44114800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:44109800-44115600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:44109800-44115800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:44109800-44115800	Weak transcription	HSMMtube	muscle
21	chr15:44109800-44116000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:44110000-44114600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:44110000-44115400	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:44110000-44115600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:44110000-44115600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:44110000-44115600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:44110000-44115600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:44110000-44115600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:44110000-44115600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:44110000-44115600	Weak transcription	Fetal Kidney	kidney
31	chr15:44110000-44115600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:44110000-44115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:44110000-44115800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:44110000-44115800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:44110000-44115800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:44110000-44115800	Weak transcription	A549	lung
37	chr15:44110000-44115800	Weak transcription	NH-A	brain
38	chr15:44110000-44115800	Weak transcription	NHDF-Ad	bronchial
39	chr15:44110200-44114600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:44110200-44114800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:44110200-44115400	Weak transcription	HMEC	breast
42	chr15:44110200-44115600	Weak transcription	Colonic Mucosa	Colon
43	chr15:44110200-44115600	Weak transcription	HSMM	muscle
44	chr15:44110200-44115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:44110200-44115800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:44110600-44115600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:44110600-44115800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:44111200-44115400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:44111200-44115400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:44111200-44115600	Weak transcription	Osteobl	bone

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