Variant report

Variant	rs1795965
Chromosome Location	chr12:122239608-122239609
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	POU2F2	chr12:122239590-122239982	GM12891	blood:	n/a	n/a
2	STAT5A	chr12:122238651-122241749	GM12878	blood:	n/a	chr12:122241725-122241737 chr12:122241729-122241741 chr12:122239925-122239937
3	POLR2A	chr12:122237649-122240329	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:122239571-122240270	GM12878	blood:	n/a	n/a
5	CHD1	chr12:122237651-122241677	IMR90	lung:	n/a	chr12:122239946-122239956 chr12:122238495-122238505
6	REST	chr12:122238388-122240079	HL-60	blood:	n/a	chr12:122238975-122238995 chr12:122239330-122239343 chr12:122238885-122238898 chr12:122238953-122238966 chr12:122238960-122238969 chr12:122239946-122239956
7	POLR2A	chr12:122234779-122241623	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr12:122237411-122240170	NB4	blood:	n/a	n/a
9	POLR2A	chr12:122234803-122242201	K562	blood:	n/a	n/a
10	POLR2A	chr12:122238814-122241184	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:122237652-122240363	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:122237348-122240348	GM12878	blood:	n/a	n/a
13	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
14	POLR2A	chr12:122239317-122242092	HCT-116	colon:	n/a	n/a
15	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
16	SPI1	chr12:122239405-122239911	HL-60	blood:	n/a	n/a
17	MXI1	chr12:122234637-122245085	SK-N-SH	brain:	n/a	n/a
18	TBP	chr12:122237079-122242074	K562	blood:	n/a	chr12:122237265-122237276
19	CHD2	chr12:122239608-122240169	H1-hESC	embryonic stem cell:	n/a	chr12:122239946-122239956
20	POLR2A	chr12:122237225-122242923	GM18505	blood:	n/a	n/a
21	POLR2A	chr12:122237473-122240029	HL-60	blood:	n/a	n/a
22	POLR2A	chr12:122234794-122240414	K562	blood:	n/a	n/a
23	MTA3	chr12:122239248-122241334	GM12878	blood:	n/a	n/a
24	NFIC	chr12:122239167-122241515	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:122237818-122241495	HUVEC	blood vessel:	n/a	n/a
26	TEAD4	chr12:122239192-122240186	K562	blood:	n/a	n/a
27	POLR2A	chr12:122236872-122242965	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:122236861-122241446	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr12:122237002-122240263	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:122239559-122240272	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:122237655-122240336	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr12:122237755-122239866	A549	lung:	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
33	POLR2A	chr12:122237373-122242890	GM19099	blood:	n/a	n/a
34	POLR2A	chr12:122231231-122242190	PANC-1	pancreas:	n/a	n/a
35	YY1	chr12:122238675-122240084	H1-hESC	embryonic stem cell:	n/a	chr12:122238941-122238955 chr12:122239000-122239017
36	POLR2A	chr12:122239569-122240037	ECC-1	luminal epithelium:	n/a	n/a
37	TBP	chr12:122237655-122241987	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr12:122238768-122240405	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr12:122234878-122240352	K562	blood:	n/a	n/a
40	POLR2A	chr12:122237714-122241584	SK-N-SH	brain:	n/a	n/a
41	REST	chr12:122236903-122243598	H1-neurons	neurons:	n/a	chr12:122238975-122238995 chr12:122239330-122239343 chr12:122238885-122238898 chr12:122238953-122238966 chr12:122242500-122242508 chr12:122238960-122238969 chr12:122239946-122239956
42	ATF2	chr12:122239528-122241264	GM12878	blood:	n/a	n/a
43	TAF1	chr12:122237222-122239689	K562	blood:	n/a	n/a
44	BCL3	chr12:122238666-122240120	A549	lung:	n/a	chr12:122239344-122239357 chr12:122238974-122238987
45	REST	chr12:122239572-122239766	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr12:122237620-122240331	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr12:122238257-122242139	Raji	blood:	n/a	n/a
48	POLR2A	chr12:122237652-122242039	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr12:122237118-122241474	IMR90	lung:	n/a	n/a
50	POLR2A	chr12:122237326-122243015	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122237414..122239746-chr17:48943458..48945237,2	MCF-7	breast:
2	chr12:122145450..122152863-chr12:122233897..122241914,16	MCF-7	breast:
3	chr12:122063594..122065295-chr12:122238095..122240834,2	K562	blood:
4	chr12:122237332..122242839-chr17:57920693..57925352,4	MCF-7	breast:
5	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
6	chr12:122188399..122190349-chr12:122238122..122239651,2	K562	blood:
7	chr12:122018588..122021080-chr12:122238013..122240517,2	MCF-7	breast:
8	chr12:122239058..122240920-chr2:174827719..174830077,2	MCF-7	breast:
9	chr12:122238900..122240438-chr6:136610251..136612271,2	MCF-7	breast:
10	chr1:109742058..109743867-chr12:122238277..122239989,2	MCF-7	breast:
11	chr12:121837219..121839609-chr12:122238728..122241051,2	MCF-7	breast:
12	chr12:122238079..122240131-chr17:59487111..59490038,2	MCF-7	breast:
13	chr12:122184835..122196012-chr12:122235281..122245445,27	MCF-7	breast:
14	chr12:122237348..122239673-chr20:55840196..55842949,3	MCF-7	breast:
15	chr12:122239049..122240564-chr12:122299953..122302949,2	K562	blood:
16	chr12:122236783..122240484-chr12:122457021..122461932,5	MCF-7	breast:
17	chr11:118965715..118967362-chr12:122238172..122240482,2	MCF-7	breast:
18	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
19	chr12:122239215..122242374-chr17:57923941..57927406,3	MCF-7	breast:
20	chr12:122238562..122240078-chr20:52823765..52826004,2	MCF-7	breast:
21	chr12:122063273..122066310-chr12:122238266..122240909,4	MCF-7	breast:
22	chr1:180122867..180124515-chr12:122237701..122240027,2	MCF-7	breast:
23	chr12:122237524..122241121-chr12:122501436..122503777,3	K562	blood:
24	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
25	chr12:122238688..122240991-chr6:27775066..27777926,2	MCF-7	breast:
26	chr12:122238851..122241051-chr8:145148871..145151481,2	MCF-7	breast:
27	chr12:122237430..122243628-chr12:122458689..122463112,11	MCF-7	breast:
28	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
29	chr12:122148639..122153380-chr12:122238008..122242328,5	MCF-7	breast:
30	chr12:122238420..122240403-chr5:140026745..140028353,2	MCF-7	breast:
31	chr12:122237524..122241320-chr12:122500575..122503777,5	K562	blood:

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

Variant related genes	Relation type
SETD1B	TF binding region
ENSG00000212694	TF binding region
RHOF	TF binding region
ENSG00000116299	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000170633	Chromatin interaction
ENSG00000029363	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000113141	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000264052	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000158104	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000255856	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000131495	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000188486	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000179091	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004390	0.93[EUR][1000 genomes]
rs11043202	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043203	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043207	0.82[EUR][1000 genomes]
rs1168663	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168664	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168665	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168666	0.95[EUR][1000 genomes]
rs1168668	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168669	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168671	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168672	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168673	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12307227	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313997	0.89[ASN][1000 genomes]
rs12314801	0.89[ASN][1000 genomes]
rs12820413	0.82[ASN][1000 genomes]
rs12823194	0.86[EUR][1000 genomes]
rs1667578	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1667579	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1795966	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2019561	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019562	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2122266	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2707057	0.82[ASN][1000 genomes]
rs2707066	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2707067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712852	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7957564	0.93[EUR][1000 genomes]
rs7974348	0.94[EUR][1000 genomes]
rs895951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895952	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895953	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895954	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs895957	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921286	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921287	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921288	0.81[EUR][1000 genomes]
rs930665	0.94[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
rs1795965	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	chr12:122236800-122245000	Active TSS	Aorta	Aorta
4	chr12:122237000-122240000	Active TSS	Gastric	stomach
5	chr12:122237000-122240800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:122237000-122243800	Active TSS	Psoas Muscle	Psoas
7	chr12:122237200-122241600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:122237200-122243800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:122237200-122243800	Active TSS	Brain Angular Gyrus	brain
10	chr12:122237200-122243800	Active TSS	Esophagus	oesophagus
11	chr12:122237200-122243800	Active TSS	Left Ventricle	heart
12	chr12:122237200-122243800	Active TSS	Right Ventricle	heart
13	chr12:122237200-122243800	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr12:122237200-122244600	Active TSS	Small Intestine	intestine
15	chr12:122237400-122243600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:122237400-122243600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:122237400-122243600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr12:122237400-122243800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:122237400-122243800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr12:122237400-122243800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:122237400-122243800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:122237400-122243800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:122237400-122243800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr12:122237400-122243800	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr12:122237400-122243800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:122237400-122243800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr12:122237400-122243800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr12:122237400-122243800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:122237400-122243800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:122237400-122243800	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr12:122237400-122243800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:122237400-122243800	Active TSS	Liver	Liver
33	chr12:122237400-122243800	Active TSS	Colon Smooth Muscle	Colon
34	chr12:122237400-122243800	Active TSS	Duodenum Mucosa	Duodenum
35	chr12:122237400-122243800	Active TSS	Fetal Brain Female	brain
36	chr12:122237400-122243800	Active TSS	Fetal Intestine Large	intestine
37	chr12:122237400-122243800	Active TSS	Pancreas	Pancrea
38	chr12:122237400-122243800	Active TSS	Rectal Smooth Muscle	rectum
39	chr12:122237400-122243800	Active TSS	GM12878-XiMat	blood
40	chr12:122237400-122243800	Active TSS	K562	blood
41	chr12:122237400-122244400	Active TSS	Thymus	Thymus
42	chr12:122237400-122244600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr12:122237600-122240000	Active TSS	Primary T cells from cord blood	blood
44	chr12:122237600-122240000	Active TSS	Spleen	Spleen
45	chr12:122237600-122240000	Active TSS	Hela-S3	cervix
46	chr12:122237600-122240400	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr12:122237600-122240600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:122237600-122241600	Active TSS	Stomach Mucosa	stomach
49	chr12:122237600-122242600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:122237600-122243600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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