Variant report

Variant	rs1795966
Chromosome Location	chr12:122238300-122238301
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	FOXA2	chr12:122237290-122238345	A549	lung:	n/a	n/a
2	EP300	chr12:122237123-122238502	T-47D	breast:	n/a	chr12:122237618-122237634 chr12:122238028-122238044 chr12:122238027-122238043
3	TEAD4	chr12:122237764-122238498	SK-N-SH	brain:	n/a	n/a
4	SIN3A	chr12:122237231-122238494	H1-hESC	embryonic stem cell:	n/a	chr12:122237618-122237629
5	EGR1	chr12:122237641-122238437	HCT-116	colon:	n/a	chr12:122237972-122237986 chr12:122238145-122238155 chr12:122237996-122238010
6	POLR2A	chr12:122237649-122240329	GM12891	blood:	n/a	n/a
7	EP300	chr12:122236930-122238478	A549	lung:	n/a	chr12:122237618-122237634 chr12:122238028-122238044 chr12:122238027-122238043
8	SMARCB1	chr12:122237254-122239415	Hela-S3	cervix:	n/a	n/a
9	CHD1	chr12:122237651-122241677	IMR90	lung:	n/a	chr12:122239946-122239956 chr12:122238495-122238505
10	MAX	chr12:122237963-122239563	ECC-1	luminal epithelium:	n/a	chr12:122238516-122238525 chr12:122239330-122239340
11	SIN3AK20	chr12:122237208-122238499	MCF-7	breast:	n/a	n/a
12	POLR2A	chr12:122234779-122241623	PANC-1	pancreas:	n/a	n/a
13	TFAP2C	chr12:122237736-122238625	Hela-S3	cervix:	n/a	n/a
14	PML	chr12:122237267-122238404	K562	blood:	n/a	n/a
15	POLR2A	chr12:122237411-122240170	NB4	blood:	n/a	n/a
16	ETS1	chr12:122237818-122238723	GM12878	blood:	n/a	chr12:122238345-122238356 chr12:122238068-122238079 chr12:122238383-122238393
17	REST	chr12:122237869-122238332	SK-N-SH	brain:	n/a	n/a
18	TAF1	chr12:122237804-122238601	SK-N-SH	brain:	n/a	n/a
19	JUND	chr12:122237599-122238681	MCF-7	breast:	n/a	chr12:122237627-122237636 chr12:122237624-122237633 chr12:122237625-122237634 chr12:122238064-122238073 chr12:122238349-122238358 chr12:122237626-122237635 chr12:122238274-122238283 chr12:122238006-122238017
20	JUND	chr12:122237694-122238413	A549	lung:	n/a	chr12:122238064-122238073 chr12:122238349-122238358 chr12:122238274-122238283 chr12:122238006-122238017
21	GATA3	chr12:122237158-122239271	A549	lung:	n/a	chr12:122238803-122238813
22	POLR2A	chr12:122237661-122238475	PFSK-1	brain:	n/a	n/a
23	MAX	chr12:122237865-122239062	A549	lung:	n/a	chr12:122238516-122238525
24	HNF4A	chr12:122237906-122238361	HepG2	liver:	n/a	n/a
25	RELA	chr12:122237812-122239269	GM12891	blood:	n/a	n/a
26	EP300	chr12:122238074-122238368	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:122238137-122238314	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUND	chr12:122237811-122238550	H1-hESC	embryonic stem cell:	n/a	chr12:122238064-122238073 chr12:122238349-122238358 chr12:122238274-122238283 chr12:122238006-122238017
29	POLR2A	chr12:122234803-122242201	K562	blood:	n/a	n/a
30	MAX	chr12:122237968-122239121	HepG2	liver:	n/a	chr12:122238516-122238525
31	POLR2A	chr12:122237652-122240363	Hela-S3	cervix:	n/a	n/a
32	SP1	chr12:122237659-122238332	K562	blood:	n/a	chr12:122238271-122238283 chr12:122238062-122238071 chr12:122238066-122238078 chr12:122238273-122238282 chr12:122238061-122238072 chr12:122238272-122238281 chr12:122238170-122238184 chr12:122238061-122238073 chr12:122238067-122238076 chr12:122238271-122238283
33	POLR2A	chr12:122237348-122240348	GM12878	blood:	n/a	n/a
34	PBX3	chr12:122237277-122238385	A549	lung:	n/a	chr12:122237577-122237597
35	POLR2A	chr12:122237781-122239516	GM12878	blood:	n/a	n/a
36	JUND	chr12:122237659-122238314	SK-N-SH	brain:	n/a	chr12:122238064-122238073 chr12:122238274-122238283 chr12:122238006-122238017
37	YY1	chr12:122237802-122240042	K562	blood:	n/a	chr12:122238941-122238955 chr12:122238063-122238077 chr12:122238598-122238620 chr12:122238344-122238358 chr12:122238449-122238463 chr12:122239000-122239017 chr12:122238514-122238528
38	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
39	GABPA	chr12:122237865-122238346	SK-N-SH	brain:	n/a	chr12:122238068-122238077
40	TCF12	chr12:122237141-122238503	ECC-1	luminal epithelium:	n/a	chr12:122237372-122237382
41	POLR2A	chr12:122237643-122239558	A549	lung:	n/a	n/a
42	RXRA	chr12:122237834-122238664	HepG2	liver:	n/a	chr12:122238299-122238306
43	TAF1	chr12:122237702-122238776	HepG2	liver:	n/a	n/a
44	E2F6	chr12:122237867-122239210	K562	blood:	n/a	chr12:122238068-122238077 chr12:122238604-122238614 chr12:122238612-122238623 chr12:122238602-122238613 chr12:122238605-122238614 chr12:122238606-122238613 chr12:122238606-122238613 chr12:122238603-122238618 chr12:122238606-122238613 chr12:122238603-122238614 chr12:122238605-122238613 chr12:122238605-122238613 chr12:122239045-122239054 chr12:122238612-122238623
45	MXI1	chr12:122234637-122245085	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr12:122238045-122238488	HepG2	liver:	n/a	n/a
47	GATA3	chr12:122237710-122238359	SK-N-SH	brain:	n/a	n/a
48	TBP	chr12:122237079-122242074	K562	blood:	n/a	chr12:122237265-122237276
49	EP300	chr12:122237426-122238384	T-47D	breast:	n/a	chr12:122237618-122237634 chr12:122238028-122238044 chr12:122238027-122238043
50	POLR2A	chr12:122237225-122242923	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122237414..122239746-chr17:48943458..48945237,2	MCF-7	breast:
2	chr12:122235984..122238947-chr2:74211072..74214040,3	MCF-7	breast:
3	chr12:122237788..122238486-chr2:172290216..172290849,2	NB4	blood:
4	chr12:122145450..122152863-chr12:122233897..122241914,16	MCF-7	breast:
5	chr12:122063594..122065295-chr12:122238095..122240834,2	K562	blood:
6	chr12:122236965..122238991-chr12:122683290..122686252,2	K562	blood:
7	chr12:122237332..122242839-chr17:57920693..57925352,4	MCF-7	breast:
8	chr11:45928634..45930948-chr12:122237013..122238884,2	MCF-7	breast:
9	chr12:122237036..122238620-chr12:122459729..122461311,2	K562	blood:
10	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
11	chr12:122188399..122190349-chr12:122238122..122239651,2	K562	blood:
12	chr12:122018588..122021080-chr12:122238013..122240517,2	MCF-7	breast:
13	chr12:122237355..122238983-chr20:49411409..49413724,2	MCF-7	breast:
14	chr12:122237028..122239073-chr12:122370482..122372481,2	K562	blood:
15	chr1:109742058..109743867-chr12:122238277..122239989,2	MCF-7	breast:
16	chr12:122235892..122238477-chr2:235091344..235092959,2	MCF-7	breast:
17	chr12:122238079..122240131-chr17:59487111..59490038,2	MCF-7	breast:
18	chr12:122184835..122196012-chr12:122235281..122245445,27	MCF-7	breast:
19	chr12:122237348..122239673-chr20:55840196..55842949,3	MCF-7	breast:
20	chr12:122236783..122240484-chr12:122457021..122461932,5	MCF-7	breast:
21	chr11:118965715..118967362-chr12:122238172..122240482,2	MCF-7	breast:
22	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
23	chr12:122063273..122066310-chr12:122238266..122240909,4	MCF-7	breast:
24	chr12:122237535..122239175-chr12:122615954..122617703,2	MCF-7	breast:
25	chr1:180122867..180124515-chr12:122237701..122240027,2	MCF-7	breast:
26	chr12:122236992..122238955-chr17:57923665..57925298,2	MCF-7	breast:
27	chr12:122237524..122241121-chr12:122501436..122503777,3	K562	blood:
28	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
29	chr12:122237910..122239511-chrX:153599147..153600887,2	MCF-7	breast:
30	chr12:122237927..122238753-chr12:122985007..122985749,2	Hela-S3	cervix:
31	chr12:122237205..122238947-chr12:122709096..122710729,2	K562	blood:
32	chr12:122236856..122239163-chr12:122456320..122458969,2	K562	blood:
33	chr12:122237430..122243628-chr12:122458689..122463112,11	MCF-7	breast:
34	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
35	chr12:122148639..122153380-chr12:122238008..122242328,5	MCF-7	breast:
36	chr12:121974810..121976577-chr12:122237441..122239422,3	MCF-7	breast:
37	chr12:122237524..122241320-chr12:122500575..122503777,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOF-1	chr12:122235738-122239714	NONHSAT031462
2	lnc-RHOF-1	chr12:122237753-122238382	NONHSAT031456

Variant related genes	Relation type
SETD1B	TF binding region
ENSG00000212694	TF binding region
ENSG00000188486	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000255856	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000234776	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000158113	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000116299	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000187013	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11043202	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11043203	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1168663	0.81[AMR][1000 genomes]
rs1168664	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168665	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168666	0.82[EUR][1000 genomes]
rs1168668	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1168669	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1168671	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168672	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1168673	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12307227	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1667578	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1667579	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1795965	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2019561	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2019562	0.81[EUR][1000 genomes]
rs2122266	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2707066	0.88[AMR][1000 genomes]
rs2707067	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs712852	0.83[AMR][1000 genomes]
rs7974348	0.81[EUR][1000 genomes]
rs895951	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs895952	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs895953	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs895954	0.81[EUR][1000 genomes]
rs895957	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs921286	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs921287	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs930665	0.81[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv911	chr12:122234524-122279425	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	esv3331230	chr12:122237769-122239717	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1795966	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122235200-122245400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:122235400-122239800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr12:122235800-122239400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
4	chr12:122236800-122238400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr12:122236800-122245000	Active TSS	Aorta	Aorta
6	chr12:122237000-122238400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr12:122237000-122239400	Active TSS	HSMMtube	muscle
8	chr12:122237000-122240000	Active TSS	Gastric	stomach
9	chr12:122237000-122240800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr12:122237000-122243800	Active TSS	Psoas Muscle	Psoas
11	chr12:122237200-122238400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:122237200-122239600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:122237200-122239600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:122237200-122241600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:122237200-122243800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:122237200-122243800	Active TSS	Brain Angular Gyrus	brain
17	chr12:122237200-122243800	Active TSS	Esophagus	oesophagus
18	chr12:122237200-122243800	Active TSS	Left Ventricle	heart
19	chr12:122237200-122243800	Active TSS	Right Ventricle	heart
20	chr12:122237200-122243800	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr12:122237200-122244600	Active TSS	Small Intestine	intestine
22	chr12:122237400-122239000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:122237400-122239000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:122237400-122239000	Active TSS	Muscle Satellite Cultured Cells	--
25	chr12:122237400-122239000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:122237400-122239000	Active TSS	Placenta	Placenta
27	chr12:122237400-122239000	Active TSS	HepG2	liver
28	chr12:122237400-122239000	Active TSS	NHDF-Ad	bronchial
29	chr12:122237400-122239000	Active TSS	Osteobl	bone
30	chr12:122237400-122239600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:122237400-122243600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:122237400-122243600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:122237400-122243600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:122237400-122243800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:122237400-122243800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr12:122237400-122243800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:122237400-122243800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:122237400-122243800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:122237400-122243800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr12:122237400-122243800	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr12:122237400-122243800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr12:122237400-122243800	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr12:122237400-122243800	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr12:122237400-122243800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:122237400-122243800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:122237400-122243800	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr12:122237400-122243800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr12:122237400-122243800	Active TSS	Liver	Liver
49	chr12:122237400-122243800	Active TSS	Colon Smooth Muscle	Colon
50	chr12:122237400-122243800	Active TSS	Duodenum Mucosa	Duodenum

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