Variant report

Variant	rs61928619
Chromosome Location	chr12:11323372-11323373
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	REST	chr12:11323254-11325495	H1-neurons	neurons:	n/a	chr12:11324075-11324088
2	NFIC	chr12:11323355-11324644	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:11323344-11325080	PFSK-1	brain:	n/a	n/a
4	TAL1	chr12:11323280-11324338	K562	blood:	n/a	n/a
5	GATA1	chr12:11323349-11324508	PBDE	blood:	n/a	n/a
6	POLR2A	chr12:11323147-11325377	K562	blood:	n/a	n/a
7	POLR2A	chr12:11323359-11324717	U87	brain:	n/a	n/a
8	POLR2A	chr12:11323372-11323384	HepG2	liver:	n/a	n/a
9	HCFC1	chr12:11323329-11325360	Hela-S3	cervix:	n/a	n/a
10	IRF1	chr12:11323346-11324725	K562	blood:	n/a	chr12:11323766-11323780 chr12:11324505-11324519 chr12:11324237-11324246 chr12:11324506-11324522

No.	Distal block	Cell Line	Cell type
1	chr12:11091072..11093170-chr12:11322389..11325259,3	MCF-7	breast:
2	chr12:11321289..11323850-chr12:11635988..11637922,2	MCF-7	breast:
3	chr12:10365255..10367563-chr12:11322614..11325373,2	K562	blood:
4	chr12:11307789..11310150-chr12:11322132..11323842,2	MCF-7	breast:
5	chr12:11322782..11326787-chr12:11332516..11335699,5	K562	blood:
6	chr12:11321748..11327565-chr12:11327784..11333912,14	MCF-7	breast:
7	chr12:11305022..11306977-chr12:11320566..11323484,2	MCF-7	breast:
8	chr12:11322432..11324431-chr12:72056353..72059109,2	MCF-7	breast:
9	chr12:10961808..10964056-chr12:11322515..11324346,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256537	TF binding region
ENSG00000133858	Chromatin interaction
ENSG00000139112	Chromatin interaction
ENSG00000255958	Chromatin interaction
ENSG00000173451	Chromatin interaction
ENSG00000256629	Chromatin interaction
ENSG00000212127	Chromatin interaction
ENSG00000121381	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs1047709	0.82[ASN][1000 genomes]
rs1047712	0.80[ASN][1000 genomes]
rs11557132	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1376742	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1451765	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1451772	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551191	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1551192	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1650020	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1650029	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1650030	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1650031	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1650053	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1669410	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669412	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669414	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669418	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669422	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1817104	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1823663	0.88[ASN][1000 genomes]
rs1823664	0.88[ASN][1000 genomes]
rs1839859	0.88[ASN][1000 genomes]
rs1863848	0.81[ASN][1000 genomes]
rs2008253	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2019629	0.88[ASN][1000 genomes]
rs2019633	0.88[ASN][1000 genomes]
rs2123006	1.00[ASN][1000 genomes]
rs2123007	1.00[ASN][1000 genomes]
rs2167481	1.00[ASN][1000 genomes]
rs2218818	0.87[ASN][1000 genomes]
rs2416544	1.00[ASN][1000 genomes]
rs2416545	1.00[ASN][1000 genomes]
rs2416546	1.00[ASN][1000 genomes]
rs2416547	1.00[ASN][1000 genomes]
rs2416548	0.82[ASN][1000 genomes]
rs2416549	0.82[ASN][1000 genomes]
rs2559581	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597918	0.87[ASN][1000 genomes]
rs2597919	0.88[ASN][1000 genomes]
rs2597920	0.88[ASN][1000 genomes]
rs2597921	0.88[ASN][1000 genomes]
rs2597923	0.88[ASN][1000 genomes]
rs2597930	0.81[ASN][1000 genomes]
rs2597931	0.81[ASN][1000 genomes]
rs2599396	0.88[ASN][1000 genomes]
rs2599397	0.83[ASN][1000 genomes]
rs2599398	0.83[ASN][1000 genomes]
rs2599404	0.88[ASN][1000 genomes]
rs2600350	0.87[ASN][1000 genomes]
rs2600351	0.88[ASN][1000 genomes]
rs2600352	0.88[ASN][1000 genomes]
rs2600353	0.88[ASN][1000 genomes]
rs2600354	0.88[ASN][1000 genomes]
rs2600355	0.84[ASN][1000 genomes]
rs2600357	0.88[ASN][1000 genomes]
rs2600359	0.83[ASN][1000 genomes]
rs2600361	0.82[ASN][1000 genomes]
rs2600363	0.83[ASN][1000 genomes]
rs2600364	0.82[ASN][1000 genomes]
rs2708331	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708343	0.82[ASN][1000 genomes]
rs2708344	0.82[ASN][1000 genomes]
rs2708345	0.81[ASN][1000 genomes]
rs2708350	0.82[ASN][1000 genomes]
rs2708368	0.87[ASN][1000 genomes]
rs2708369	0.87[ASN][1000 genomes]
rs2708370	0.88[ASN][1000 genomes]
rs2923860	0.88[ASN][1000 genomes]
rs319267	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319268	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319271	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319272	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319273	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs319274	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34000114	0.87[ASN][1000 genomes]
rs34018339	1.00[ASN][1000 genomes]
rs34082341	0.87[ASN][1000 genomes]
rs34241192	0.88[ASN][1000 genomes]
rs34270405	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34288418	0.88[ASN][1000 genomes]
rs34327967	0.88[ASN][1000 genomes]
rs34436598	0.87[ASN][1000 genomes]
rs34444884	0.82[ASN][1000 genomes]
rs34531956	1.00[ASN][1000 genomes]
rs34536990	0.88[ASN][1000 genomes]
rs34548551	0.88[ASN][1000 genomes]
rs34590962	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34685506	0.88[ASN][1000 genomes]
rs34769150	0.88[ASN][1000 genomes]
rs34843817	0.88[ASN][1000 genomes]
rs34927715	0.88[ASN][1000 genomes]
rs35017789	0.87[ASN][1000 genomes]
rs35021653	0.88[ASN][1000 genomes]
rs35119575	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35124606	0.88[ASN][1000 genomes]
rs35151793	1.00[ASN][1000 genomes]
rs35183723	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35267335	0.81[AFR][1000 genomes]
rs35280352	0.88[ASN][1000 genomes]
rs35326227	0.80[ASN][1000 genomes]
rs35340812	0.88[ASN][1000 genomes]
rs35699328	0.88[ASN][1000 genomes]
rs35813024	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35856529	0.87[ASN][1000 genomes]
rs35893804	0.88[ASN][1000 genomes]
rs36050405	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36062343	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36115011	0.88[ASN][1000 genomes]
rs3906996	0.88[ASN][1000 genomes]
rs3911800	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4583064	0.82[ASN][1000 genomes]
rs4763638	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61928449	0.86[ASN][1000 genomes]
rs61928562	0.87[ASN][1000 genomes]
rs61928564	0.87[ASN][1000 genomes]
rs61928565	0.87[ASN][1000 genomes]
rs61928566	0.87[ASN][1000 genomes]
rs61928569	0.88[ASN][1000 genomes]
rs61928595	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61928597	0.88[ASN][1000 genomes]
rs61928602	0.88[ASN][1000 genomes]
rs61928610	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61928618	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928642	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928643	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928644	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61928646	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61931266	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs61931270	0.88[ASN][1000 genomes]
rs61931274	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61931278	0.85[ASN][1000 genomes]
rs61931279	0.87[ASN][1000 genomes]
rs6488347	0.89[ASN][1000 genomes]
rs6488348	0.89[ASN][1000 genomes]
rs6488349	0.89[ASN][1000 genomes]
rs6488350	0.89[ASN][1000 genomes]
rs6488351	0.88[ASN][1000 genomes]
rs6488355	0.88[ASN][1000 genomes]
rs6488356	0.88[ASN][1000 genomes]
rs7298544	0.87[ASN][1000 genomes]
rs7302010	0.88[ASN][1000 genomes]
rs7310047	0.88[ASN][1000 genomes]
rs7313796	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7350611	0.81[ASN][1000 genomes]
rs7486717	0.88[ASN][1000 genomes]
rs7488095	0.82[ASN][1000 genomes]
rs7488102	0.80[ASN][1000 genomes]
rs7955495	0.88[ASN][1000 genomes]
rs7959320	0.88[ASN][1000 genomes]
rs7960823	0.88[ASN][1000 genomes]
rs7965506	0.88[ASN][1000 genomes]
rs7969625	1.00[ASN][1000 genomes]
rs7970225	0.86[ASN][1000 genomes]
rs7973730	0.88[ASN][1000 genomes]
rs7976211	0.88[ASN][1000 genomes]
rs8300	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977473	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
7	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv1042134	chr12:11220712-11328131	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs61928619	RP11-434C1.1	cis	lung	GTEx
rs61928619	TAS2R14	cis	Nerve Tibial	GTEx
rs61928619	PRR4	cis	lung	GTEx
rs61928619	PRR4	cis	Nerve Tibial	GTEx
rs61928619	RP11-434C1.1	cis	Heart Left Ventricle	GTEx
rs61928619	PRR4	cis	Whole Blood	GTEx
rs61928619	PRR4	cis	Thyroid	GTEx
rs61928619	PRR4	cis	Artery Tibial	GTEx
rs61928619	RP11-434C1.1	cis	Nerve Tibial	GTEx
rs61928619	PRR4	cis	Heart Left Ventricle	GTEx
rs61928619	PRR4	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11303800-11323600	Weak transcription	Esophagus	oesophagus
2	chr12:11304000-11323600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:11312000-11323400	Weak transcription	Stomach Mucosa	stomach
4	chr12:11313800-11323600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:11319200-11323400	Weak transcription	Placenta	Placenta
6	chr12:11319200-11323600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:11319200-11323600	Weak transcription	Lung	lung
8	chr12:11319600-11323600	Weak transcription	Ovary	ovary
9	chr12:11319600-11323800	Weak transcription	Spleen	Spleen
10	chr12:11321000-11323400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr12:11321200-11323400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr12:11321200-11323400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:11321200-11323400	Enhancers	Left Ventricle	heart
14	chr12:11321200-11323600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr12:11321600-11323600	Enhancers	Small Intestine	intestine
16	chr12:11321800-11323400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:11321800-11323400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:11321800-11323800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:11322000-11323400	Enhancers	Pancreas	Pancrea
20	chr12:11322200-11323400	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:11322200-11323400	Weak transcription	Aorta	Aorta
22	chr12:11322200-11326000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:11322400-11323400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:11322400-11323400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:11322400-11324800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:11322400-11325800	Active TSS	K562	blood
27	chr12:11322600-11323400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr12:11322600-11323400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:11322600-11325600	Active TSS	HSMMtube	muscle
30	chr12:11322800-11323400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:11322800-11323400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:11322800-11323400	Enhancers	Fetal Muscle Trunk	muscle
33	chr12:11322800-11323400	Flanking Active TSS	Dnd41	blood
34	chr12:11322800-11323600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:11322800-11325000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:11322800-11325200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:11322800-11325200	Active TSS	Stomach Smooth Muscle	stomach
38	chr12:11322800-11325400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr12:11322800-11325400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:11322800-11325400	Active TSS	A549	lung
41	chr12:11322800-11325600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:11322800-11325600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:11322800-11325800	Active TSS	GM12878-XiMat	blood
44	chr12:11322800-11326200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr12:11323000-11323400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:11323000-11323400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr12:11323000-11323400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:11323000-11323400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr12:11323000-11323400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:11323000-11323400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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