Variant report

Variant	rs4078141
Chromosome Location	chr5:179051538-179051539
allele	A/G
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	SPI1	chr5:179050996-179051740	GM12878	blood:	n/a	chr5:179051306-179051315 chr5:179051304-179051317
2	POLR2A	chr5:179049682-179051896	K562	blood:	n/a	n/a
3	POLR2A	chr5:179049958-179051787	GM12891	blood:	n/a	n/a
4	MAX	chr5:179049581-179052171	K562	blood:	n/a	n/a
5	MAX	chr5:179051336-179051880	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:179047206-179051952	GM12878	blood:	n/a	n/a
7	TBP	chr5:179050438-179051837	Hela-S3	cervix:	n/a	n/a
8	YY1	chr5:179049647-179051700	GM12892	blood:	n/a	chr5:179051234-179051245 chr5:179050403-179050412 chr5:179050398-179050408 chr5:179050406-179050420 chr5:179051155-179051164
9	MAX	chr5:179049681-179051857	Hela-S3	cervix:	n/a	n/a
10	MAZ	chr5:179049655-179052146	K562	blood:	n/a	n/a
11	POLR2A	chr5:179049656-179052058	K562	blood:	n/a	n/a
12	NR2F2	chr5:179051415-179052087	K562	blood:	n/a	n/a
13	POLR2A	chr5:179050099-179051751	HepG2	liver:	n/a	n/a
14	E2F6	chr5:179050534-179051604	H1-hESC	embryonic stem cell:	n/a	chr5:179050941-179050950 chr5:179050880-179050889 chr5:179050774-179050783 chr5:179050891-179050905 chr5:179051155-179051164 chr5:179050721-179050730
15	POLR2A	chr5:179049692-179051794	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr5:179049295-179051786	MCF10A-Er-Src	breast:	n/a	n/a
17	TAF1	chr5:179051486-179051777	GM12878	blood:	n/a	n/a
18	ATF2	chr5:179051421-179051783	GM12878	blood:	n/a	n/a
19	UBTF	chr5:179051131-179051793	K562	blood:	n/a	n/a
20	CREB1	chr5:179049564-179051780	HepG2	liver:	n/a	n/a
21	FOS	chr5:179051462-179051801	MCF10A-Er-Src	breast:	n/a	n/a
22	PML	chr5:179049576-179051610	MCF-7	breast:	n/a	n/a
23	POLR2A	chr5:179049984-179051776	GM12891	blood:	n/a	n/a
24	ZNF263	chr5:179050074-179051594	HEK293-T-REx	kidney:	n/a	n/a
25	POLR2A	chr5:179049950-179051791	Hela-S3	cervix:	n/a	n/a
26	MAX	chr5:179050447-179051825	HepG2	liver:	n/a	n/a
27	POLR2A	chr5:179050876-179051849	H1-hESC	embryonic stem cell:	n/a	n/a
28	CUX1	chr5:179051382-179051622	GM12878	blood:	n/a	n/a
29	NFIC	chr5:179049947-179051552	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:179049614-179051921	HL-60	blood:	n/a	n/a
31	FOSL2	chr5:179051367-179051842	SK-N-SH	brain:	n/a	n/a
32	SMC3	chr5:179051297-179051955	Hela-S3	cervix:	n/a	n/a
33	E2F6	chr5:179049764-179051771	K562	blood:	n/a	chr5:179050941-179050950 chr5:179050880-179050889 chr5:179050774-179050783 chr5:179050891-179050905 chr5:179051155-179051164 chr5:179050417-179050426 chr5:179050721-179050730
34	REST	chr5:179049955-179051916	HL-60	blood:	n/a	chr5:179050524-179050537 chr5:179050524-179050544 chr5:179050527-179050540
35	POLR2A	chr5:179050897-179051702	HepG2	liver:	n/a	n/a
36	POLR2A	chr5:179049664-179051863	ECC-1	luminal epithelium:	n/a	n/a
37	TEAD4	chr5:179049946-179052101	K562	blood:	n/a	n/a
38	MAX	chr5:179049640-179051743	ECC-1	luminal epithelium:	n/a	n/a
39	CHD1	chr5:179047686-179052125	IMR90	lung:	n/a	chr5:179050801-179050811 chr5:179051151-179051161
40	TBP	chr5:179049778-179051672	H1-hESC	embryonic stem cell:	n/a	n/a
41	RCOR1	chr5:179050435-179052086	K562	blood:	n/a	n/a
42	E2F6	chr5:179050137-179051876	Hela-S3	cervix:	n/a	chr5:179050941-179050950 chr5:179050880-179050889 chr5:179050774-179050783 chr5:179050891-179050905 chr5:179051155-179051164 chr5:179050417-179050426 chr5:179050721-179050730
43	HEY1	chr5:179049980-179051739	K562	blood:	n/a	n/a
44	MAFK	chr5:179050426-179051910	Hela-S3	cervix:	n/a	chr5:179051841-179051861 chr5:179051301-179051316
45	POLR2A	chr5:179049521-179051682	A549	lung:	n/a	n/a
46	POLR2A	chr5:179049997-179051808	HCT-116	colon:	n/a	n/a
47	PML	chr5:179049938-179051810	K562	blood:	n/a	n/a
48	POU2F2	chr5:179049872-179051790	GM12878	blood:	n/a	n/a
49	RCOR1	chr5:179049692-179051781	Hela-S3	cervix:	n/a	n/a
50	MAX	chr5:179049664-179052175	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:69753495..69755844-chr5:179048677..179051620,2	MCF-7	breast:
2	chr5:178993088..178996882-chr5:179048174..179052059,4	K562	blood:
3	chr5:179051109..179052652-chr5:179157575..179159893,2	K562	blood:
4	chr5:179049088..179052063-chr5:179245796..179250145,6	MCF-7	breast:
5	chr5:179003044..179005228-chr5:179048934..179051877,3	K562	blood:
6	chr5:179047278..179052613-chr5:179246048..179251997,13	K562	blood:
7	chr14:75745270..75745773-chr5:179050980..179051651,2	Hela-S3	cervix:
8	chr5:178985192..178988541-chr5:179048594..179052191,5	MCF-7	breast:
9	chr5:178882272..178884920-chr5:179049238..179052060,2	K562	blood:
10	chr5:178976591..178978128-chr5:179049452..179051597,2	MCF-7	breast:
11	chr5:179047637..179052326-chr5:179245599..179249536,7	K562	blood:
12	chr5:179023314..179026919-chr5:179048927..179051890,4	MCF-7	breast:
13	chr5:178986094..178988194-chr5:179049451..179052935,4	MCF-7	breast:
14	chr5:179049208..179051645-chr5:179125705..179129690,6	MCF-7	breast:
15	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
16	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
17	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
18	chr12:7072083..7074369-chr5:179050327..179052683,2	MCF-7	breast:
19	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
20	chr17:7387555..7388114-chr5:179050649..179051622,2	Hela-S3	cervix:
21	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
22	chr17:73178705..73180897-chr5:179050924..179052648,2	MCF-7	breast:
23	chr5:179048548..179052839-chr5:179221765..179224480,6	MCF-7	breast:
24	chr5:179049048..179052854-chr5:179122221..179127718,16	MCF-7	breast:
25	chr5:179050119..179051814-chr5:179134702..179137215,4	MCF-7	breast:
26	chr5:179049837..179051764-chr5:179334057..179336513,2	MCF-7	breast:
27	chr5:179047558..179053114-chr5:179123905..179129187,22	K562	blood:
28	chr1:202857623..202858300-chr5:179051524..179052025,2	Hela-S3	cervix:
29	chr11:62609117..62609653-chr5:179050747..179051683,2	NB4	blood:
30	chr5:179049195..179052432-chr5:179232038..179235083,3	K562	blood:
31	chr5:179049252..179051807-chr5:179078099..179079783,3	MCF-7	breast:
32	chr5:179048168..179052824-chr5:179156969..179161337,9	MCF-7	breast:
33	chr5:179049533..179052334-chr5:179104256..179107492,4	MCF-7	breast:
34	chr5:179049533..179051991-chr5:180649079..180651158,2	MCF-7	breast:
35	chr2:61403577..61406142-chr5:179049162..179051575,2	MCF-7	breast:
36	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:
37	chr5:178992676..178996882-chr5:179050015..179052234,4	K562	blood:

Variant related genes	Relation type
HNRNPH1	TF binding region
ENSG00000181222	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000245750	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000257084	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000207713	Chromatin interaction
ENSG00000259215	Chromatin interaction
ENSG00000188612	Chromatin interaction
ENSG00000271969	Chromatin interaction
ENSG00000204659	Chromatin interaction
ENSG00000264732	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000228259	Chromatin interaction
ENSG00000250674	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000173209	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000207708	Chromatin interaction
ENSG00000146063	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000183155	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10066669	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10076293	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1136267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13162707	0.87[ASN][1000 genomes]
rs28544040	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4131080	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4336318	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs4376229	0.86[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs4563584	0.83[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4701143	0.80[JPT][hapmap]
rs6876679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7448707	0.80[JPT][hapmap]

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	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' 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	312 gene(s)	inside rSNPs	diseases
4	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv883273	chr5:179045142-179086833	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
6	nsv823357	chr5:179046318-179058193	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4078141	RUFY1	cis	cerebellum	SCAN
rs4078141	PDLIM7	cis	parietal	SCAN
rs4078141	HNRPH1	cis	multi-tissue	Pritchard
rs4078141	HNRNPH1	cis	lymphoblastoid	seeQTL
rs4078141	HNRNPH1	cis	Liver	GTEx
rs4078141	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs4078141	HNRNPH1	cis	Lymphoblastoid	GTEx
rs4078141	HNRNPH1	cis	parietal	SCAN
rs4078141	RUFY1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179048000-179051800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr5:179048200-179051600	Active TSS	Ovary	ovary
3	chr5:179049000-179051600	Active TSS	Aorta	Aorta
4	chr5:179049000-179051600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr5:179049000-179051600	Active TSS	Esophagus	oesophagus
6	chr5:179049000-179051600	Active TSS	Psoas Muscle	Psoas
7	chr5:179049000-179051600	Active TSS	Small Intestine	intestine
8	chr5:179049000-179051800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:179049200-179051600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr5:179049200-179051600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr5:179049200-179051600	Active TSS	Liver	Liver
12	chr5:179049200-179051600	Active TSS	Brain Anterior Caudate	brain
13	chr5:179049200-179051600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:179049200-179051600	Active TSS	Brain Substantia Nigra	brain
15	chr5:179049200-179051600	Active TSS	Colon Smooth Muscle	Colon
16	chr5:179049200-179051600	Active TSS	Stomach Mucosa	stomach
17	chr5:179049400-179051600	Active TSS	Brain Cingulate Gyrus	brain
18	chr5:179049400-179051600	Active TSS	Fetal Kidney	kidney
19	chr5:179049800-179051600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr5:179049800-179051800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:179049800-179051800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:179050000-179051600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:179050000-179051600	Bivalent/Poised TSS	HepG2	liver
24	chr5:179050200-179051800	Transcr. at gene 5' and 3'	Right Atrium	heart
25	chr5:179050600-179051600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:179051000-179051600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:179051000-179051600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr5:179051000-179051600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:179051000-179051600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:179051000-179051800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:179051000-179051800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr5:179051000-179051800	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr5:179051000-179051800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr5:179051000-179051800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr5:179051000-179051800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr5:179051000-179051800	Flanking Active TSS	Placenta	Placenta
37	chr5:179051000-179051800	Flanking Active TSS	HMEC	breast
38	chr5:179051000-179052000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:179051000-179052000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr5:179051000-179052000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr5:179051000-179052000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:179051000-179052000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr5:179051000-179052000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:179051000-179052000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:179051000-179052000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr5:179051000-179052000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr5:179051000-179052000	Flanking Active TSS	HUVEC	blood vessel
48	chr5:179051000-179052000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr5:179051000-179052000	Flanking Active TSS	NH-A	brain
50	chr5:179051000-179052000	Flanking Active TSS	Osteobl	bone

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