Variant report

Variant	rs3811453
Chromosome Location	chr1:154194579-154194580
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	POLR2A	chr1:154192263-154194664	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:154191926-154194626	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr1:154191823-154194934	IMR90	lung:	n/a	chr1:154193182-154193191
4	CREB1	chr1:154192479-154194590	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:154191617-154194627	GM12892	blood:	n/a	n/a
6	CHD1	chr1:154191005-154195527	IMR90	lung:	n/a	n/a
7	GTF2F1	chr1:154193767-154194587	Hela-S3	cervix:	n/a	n/a
8	WRNIP1	chr1:154193840-154194737	GM12878	blood:	n/a	n/a
9	KAP1	chr1:154194477-154196011	K562	blood:	n/a	n/a
10	POLR2A	chr1:154191401-154194659	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:154194004-154194684	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:154191381-154195966	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:154190224-154195227	MCF10A-Er-Src	breast:	n/a	n/a
14	REST	chr1:154192439-154194608	H1-neurons	neurons:	n/a	chr1:154194100-154194120 chr1:154192923-154192936
15	HCFC1	chr1:154190865-154194751	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:154194353-154194646	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:154190805-154194605	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr1:154191740-154194885	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:154191720-154195268	GM12878	blood:	n/a	n/a
20	SIN3A	chr1:154192049-154194605	H1-hESC	embryonic stem cell:	n/a	chr1:154193416-154193429
21	POLR2A	chr1:154191910-154194585	GM12892	blood:	n/a	n/a
22	HEY1	chr1:154191986-154194658	K562	blood:	n/a	chr1:154193761-154193776
23	POLR2A	chr1:154188430-154195179	SK-N-MC	brain:	n/a	n/a
24	MXI1	chr1:154191472-154195320	SK-N-SH	brain:	n/a	chr1:154193182-154193191
25	MAZ	chr1:154191409-154195422	IMR90	lung:	n/a	chr1:154193183-154193192 chr1:154193761-154193771 chr1:154193183-154193192 chr1:154193398-154193411 chr1:154193183-154193192 chr1:154193182-154193193 chr1:154193400-154193409 chr1:154193091-154193100 chr1:154193400-154193409 chr1:154193399-154193410 chr1:154193979-154193988 chr1:154193086-154193105 chr1:154193398-154193411 chr1:154193091-154193100
26	POLR2A	chr1:154191604-154195326	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr1:154193636-154194626	U87	brain:	n/a	n/a
28	TAF1	chr1:154192422-154194642	H1-neurons	neurons:	n/a	n/a
29	REST	chr1:154192060-154195070	H1-neurons	neurons:	n/a	chr1:154194100-154194120 chr1:154192923-154192936
30	JUN	chr1:154192449-154195320	K562	blood:	n/a	chr1:154192702-154192716 chr1:154193096-154193104
31	POLR2A	chr1:154192131-154194812	Hela-S3	cervix:	n/a	n/a
32	PML	chr1:154191953-154194691	GM12878	blood:	n/a	n/a
33	TBP	chr1:154194057-154194768	Hela-S3	cervix:	n/a	n/a
34	MYC	chr1:154191933-154194761	A549	lung:	n/a	chr1:154193183-154193192 chr1:154193761-154193771 chr1:154193183-154193192 chr1:154193398-154193411 chr1:154193183-154193192 chr1:154193182-154193193 chr1:154193400-154193409 chr1:154193091-154193100 chr1:154193400-154193409 chr1:154193399-154193410 chr1:154193979-154193988 chr1:154193086-154193105 chr1:154193398-154193411 chr1:154193091-154193100
35	POLR2A	chr1:154192387-154194768	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr1:154191869-154194673	GM12892	blood:	n/a	n/a
37	IRF1	chr1:154194232-154194670	K562	blood:	n/a	n/a
38	POLR2A	chr1:154191905-154194880	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr1:154191771-154194846	PBDE	blood:	n/a	n/a
40	POLR2A	chr1:154191560-154194726	HepG2	liver:	n/a	n/a
41	TBP	chr1:154192064-154194600	K562	blood:	n/a	n/a
42	POLR2A	chr1:154192475-154194617	H1-neurons	neurons:	n/a	n/a
43	UBTF	chr1:154192540-154194635	K562	blood:	n/a	n/a
44	CHD1	chr1:154193426-154194741	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154194303..154196479-chr1:154230537..154232056,2	MCF-7	breast:
2	chr1:153916668..153920266-chr1:154191885..154196472,6	MCF-7	breast:
3	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
4	chr1:154193867..154196410-chr1:154304631..154306238,2	K562	blood:
5	chr1:154148286..154150697-chr1:154192561..154194921,2	MCF-7	breast:
6	chr1:154161421..154168420-chr1:154191340..154198003,13	MCF-7	breast:
7	chr1:154191694..154194971-chr1:154228810..154231860,3	K562	blood:
8	chr1:154151605..154157694-chr1:154191153..154195788,18	MCF-7	breast:
9	chr1:154191445..154194835-chr1:154242300..154245672,3	MCF-7	breast:
10	chr1:153936330..153941464-chr1:154191669..154195552,8	MCF-7	breast:
11	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
12	chr1:154192034..154195055-chr1:154237858..154241372,4	MCF-7	breast:
13	chr1:154193523..154195040-chr16:2203296..2205907,2	MCF-7	breast:
14	chr1:154191694..154195364-chr1:154228810..154233315,6	K562	blood:
15	chr1:154190796..154197109-chr1:154207892..154217963,21	MCF-7	breast:
16	chr1:153961938..153967162-chr1:154189861..154195978,9	K562	blood:
17	chr1:154191842..154194909-chr1:154241050..154247826,7	K562	blood:
18	chr1:154192757..154194953-chr1:154301046..154303668,3	MCF-7	breast:
19	chr1:154153643..154157449-chr1:154190048..154195510,8	K562	blood:
20	chr1:154193886..154194782-chr16:89989345..89990188,2	Hela-S3	cervix:
21	chr1:154154882..154155770-chr1:154193496..154194903,4	Hela-S3	cervix:
22	chr1:154177747..154182716-chr1:154190412..154196946,9	K562	blood:
23	chr1:154192524..154195187-chr1:154232740..154234753,2	MCF-7	breast:
24	chr1:154194086..154195833-chr1:154296026..154297621,2	K562	blood:
25	chr1:154192079..154194850-chr1:154292071..154294843,2	K562	blood:
26	chr1:153939104..153942755-chr1:154191760..154194945,4	MCF-7	breast:
27	chr1:154171859..154174380-chr1:154194428..154197108,2	MCF-7	breast:
28	chr1:154194086..154195906-chr1:154295331..154297621,3	K562	blood:
29	chr1:154193467..154195403-chr1:154225048..154228956,3	MCF-7	breast:

Variant related genes	Relation type
UBAP2L	TF binding region
C1orf43	TF binding region
ENSG00000163263	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000258947	Chromatin interaction
ENSG00000143595	Chromatin interaction
ENSG00000252817	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000131653	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000201129	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000273026	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10158820	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1044013	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs11265238	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11265251	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs11265425	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11802893	0.90[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs1194593	0.95[JPT][hapmap]
rs1194596	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs12023901	0.90[ASN][1000 genomes]
rs12025237	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12026177	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12026615	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12027999	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12028949	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12043131	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs12062977	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12135346	0.85[ASN][1000 genomes]
rs12733060	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12738393	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12742691	0.84[ASN][1000 genomes]
rs12743874	0.86[ASN][1000 genomes]
rs12749447	0.85[ASN][1000 genomes]
rs12750321	0.86[ASN][1000 genomes]
rs16835846	0.90[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs16835852	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs1760802	0.95[JPT][hapmap]
rs2274993	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2282227	0.88[ASN][1000 genomes]
rs2340473	0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2790689	0.82[JPT][hapmap]
rs28372838	0.81[EUR][1000 genomes]
rs2879788	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs34128679	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34335016	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34752019	0.82[JPT][hapmap]
rs35761479	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3762339	0.80[ASN][1000 genomes]
rs3762340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3790613	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790614	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3811455	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs3828077	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3935419	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs4240871	0.81[ASN][1000 genomes]
rs4459102	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs4620534	0.90[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs6427509	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6671009	0.82[JPT][hapmap]
rs6673752	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6676022	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6719	0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9803857	0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9943093	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	esv3339331	chr1:154192353-154194901	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3811453	DENND4B	cis	parietal	SCAN
rs3811453	SLC27A3	cis	lymphoblastoid	seeQTL
rs3811453	RAB13	cis	parietal	SCAN
rs3811453	HAX1	cis	cerebellum	SCAN
rs3811453	C1orf43	cis	parietal	SCAN
rs3811453	HAX1	cis	parietal	SCAN
rs3811453	HAX1	cis	lymphoblastoid	seeQTL
rs3811453	SCAMP3	cis	parietal	SCAN
rs3811453	PIP5K1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154191600-154194600	Active TSS	Fetal Intestine Large	intestine
2	chr1:154191600-154194600	Active TSS	Pancreas	Pancrea
3	chr1:154191600-154194800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:154191600-154194800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:154191600-154194800	Active TSS	Left Ventricle	heart
6	chr1:154191600-154195000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:154191600-154195000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:154191600-154195000	Active TSS	Psoas Muscle	Psoas
9	chr1:154191600-154195200	Active TSS	Right Ventricle	heart
10	chr1:154191600-154195400	Active TSS	GM12878-XiMat	blood
11	chr1:154191800-154194600	Active TSS	Aorta	Aorta
12	chr1:154191800-154194800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:154191800-154194800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:154191800-154194800	Active TSS	Fetal Muscle Trunk	muscle
15	chr1:154191800-154195000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:154191800-154195000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:154191800-154195000	Active TSS	NHDF-Ad	bronchial
18	chr1:154191800-154195200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:154191800-154195200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:154191800-154195400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:154191800-154195400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:154191800-154195600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:154192000-154194600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:154192000-154194600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:154192000-154194600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:154192000-154194600	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr1:154192000-154194600	Active TSS	Esophagus	oesophagus
28	chr1:154192000-154194600	Active TSS	HSMM	muscle
29	chr1:154192000-154194800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:154192000-154194800	Active TSS	Lung	lung
31	chr1:154192000-154195000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:154192000-154195000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:154192000-154195200	Active TSS	Ovary	ovary
34	chr1:154192000-154195400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:154192200-154194600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:154192200-154194600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:154192200-154194600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:154192200-154194600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:154192200-154194600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr1:154192200-154194600	Active TSS	Placenta	Placenta
41	chr1:154192200-154194600	Active TSS	Gastric	stomach
42	chr1:154192200-154194600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:154192200-154194600	Active TSS	Hela-S3	cervix
44	chr1:154192200-154194800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr1:154192200-154194800	Active TSS	NHLF	lung
46	chr1:154192200-154195000	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:154192200-154195000	Active TSS	HSMMtube	muscle
48	chr1:154192200-154195400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:154192200-154195800	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:154192400-154194600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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