Variant report

Variant	rs31978
Chromosome Location	chr5:14581556-14581557
allele	G/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	SP1	chr5:14581443-14582120	A549	lung:	n/a	chr5:14581791-14581802 chr5:14581792-14581802 chr5:14581882-14581896 chr5:14581793-14581802 chr5:14581792-14581806 chr5:14581792-14581801 chr5:14581883-14581892 chr5:14581811-14581822 chr5:14581792-14581801 chr5:14581791-14581803 chr5:14581791-14581803 chr5:14581865-14581876 chr5:14581822-14581843 chr5:14581792-14581802
2	TAF1	chr5:14581467-14582559	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF7	chr5:14581513-14582596	H1-hESC	embryonic stem cell:	n/a	n/a
4	PBX3	chr5:14581531-14582104	A549	lung:	n/a	chr5:14581836-14581856 chr5:14581832-14581841
5	ZBTB7A	chr5:14581416-14582694	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr5:14581530-14582801	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr5:14581413-14582237	H1-hESC	embryonic stem cell:	n/a	chr5:14581882-14581892
8	SP1	chr5:14581431-14582086	A549	lung:	n/a	chr5:14581791-14581802 chr5:14581792-14581802 chr5:14581882-14581896 chr5:14581793-14581802 chr5:14581792-14581806 chr5:14581792-14581801 chr5:14581883-14581892 chr5:14581811-14581822 chr5:14581792-14581801 chr5:14581791-14581803 chr5:14581791-14581803 chr5:14581865-14581876 chr5:14581822-14581843 chr5:14581792-14581802
9	RFX5	chr5:14581380-14581959	Hela-S3	cervix:	n/a	chr5:14581832-14581841
10	MXI1	chr5:14580413-14583453	SK-N-SH	brain:	n/a	n/a
11	TFAP2C	chr5:14580637-14582592	Hela-S3	cervix:	n/a	chr5:14581896-14581911 chr5:14581016-14581031
12	POLR2A	chr5:14581526-14582043	Hela-S3	cervix:	n/a	n/a
13	REST	chr5:14581334-14582917	H1-neurons	neurons:	n/a	chr5:14582204-14582214 chr5:14581990-14582003 chr5:14581746-14581764
14	CTCF	chr5:14581500-14581650	HEK293	kidney:	n/a	n/a
15	POLR2A	chr5:14581360-14582728	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr5:14581313-14582916	A549	lung:	n/a	chr5:14581882-14581892
17	E2F6	chr5:14581385-14582204	H1-hESC	embryonic stem cell:	n/a	chr5:14582122-14582131 chr5:14581720-14581732 chr5:14581833-14581842
18	ELF1	chr5:14581426-14582719	GM12878	blood:	n/a	chr5:14582224-14582236
19	MAX	chr5:14581452-14582821	ECC-1	luminal epithelium:	n/a	chr5:14581882-14581892
20	MAZ	chr5:14581525-14582197	IMR90	lung:	n/a	chr5:14581882-14581892
21	NFYB	chr5:14581385-14582010	K562	blood:	n/a	chr5:14581829-14581844 chr5:14581830-14581844 chr5:14581831-14581846 chr5:14581829-14581844 chr5:14581832-14581842 chr5:14581831-14581844
22	BACH1	chr5:14581450-14582638	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr5:14581531-14582609	Hela-S3	cervix:	n/a	chr5:14581882-14581892
24	TBP	chr5:14581400-14582720	H1-hESC	embryonic stem cell:	n/a	n/a
25	SMARCB1	chr5:14581333-14582735	Hela-S3	cervix:	n/a	n/a
26	CREB1	chr5:14581492-14582060	A549	lung:	n/a	n/a
27	TFAP2A	chr5:14580683-14582513	Hela-S3	cervix:	n/a	chr5:14581018-14581033 chr5:14581019-14581030 chr5:14581539-14581551 chr5:14582448-14582460 chr5:14582449-14582457 chr5:14581539-14581550 chr5:14581539-14581551 chr5:14581019-14581030 chr5:14581019-14581030 chr5:14582449-14582457 chr5:14582449-14582457 chr5:14581019-14581030
28	POLR2A	chr5:14581436-14582568	A549	lung:	n/a	n/a
29	ZBTB7A	chr5:14581450-14582633	ECC-1	luminal epithelium:	n/a	n/a
30	JUND	chr5:14581485-14581685	H1-hESC	embryonic stem cell:	n/a	n/a
31	PBX3	chr5:14581534-14582187	SK-N-SH	brain:	n/a	chr5:14581836-14581856 chr5:14581832-14581841
32	MXI1	chr5:14581472-14581571	Hela-S3	cervix:	n/a	n/a
33	ZNF143	chr5:14581417-14582141	H1-hESC	embryonic stem cell:	n/a	chr5:14581884-14581902
34	MAFK	chr5:14580576-14581573	Hela-S3	cervix:	n/a	chr5:14581156-14581171
35	POLR2A	chr5:14581430-14582713	Hela-S3	cervix:	n/a	n/a
36	TAF1	chr5:14581548-14582158	ECC-1	luminal epithelium:	n/a	n/a
37	NFYA	chr5:14581440-14582046	Hela-S3	cervix:	n/a	chr5:14581829-14581844 chr5:14581830-14581844 chr5:14581829-14581844 chr5:14581825-14581843 chr5:14581832-14581842 chr5:14581831-14581844
38	RCOR1	chr5:14580445-14582019	Hela-S3	cervix:	n/a	n/a
39	CHD2	chr5:14581431-14582614	Hela-S3	cervix:	n/a	chr5:14581877-14581887 chr5:14582100-14582110
40	SIN3A	chr5:14581437-14582535	H1-hESC	embryonic stem cell:	n/a	chr5:14582205-14582214 chr5:14581750-14581764
41	PBX3	chr5:14581489-14582051	SK-N-SH	brain:	n/a	chr5:14581836-14581856 chr5:14581832-14581841
42	SP1	chr5:14581490-14582155	HCT-116	colon:	n/a	chr5:14581791-14581802 chr5:14581792-14581802 chr5:14581882-14581896 chr5:14581793-14581802 chr5:14581792-14581806 chr5:14581792-14581801 chr5:14581883-14581892 chr5:14581811-14581822 chr5:14581792-14581801 chr5:14581791-14581803 chr5:14582121-14582133 chr5:14581791-14581803 chr5:14581865-14581876 chr5:14581822-14581843 chr5:14581792-14581802

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:14581529-14581579	AG04449	skin:	fetal
2	chr5:14581529-14581579	Hela-S3	cervix:	n/a
3	chr5:14581529-14581579	HEEpiC	esophagus:	n/a
4	chr5:14581529-14581579	GM06990	blood:	n/a
5	chr5:14581529-14581579	HIPEpiC	eye:	n/a
6	chr5:14581529-14581579	A549	lung:	n/a
7	chr5:14581529-14581579	SK-N-SH_RA	brain:	n/a
8	chr5:14581529-14581579	PrEC	prostate:	n/a
9	chr5:14581529-14581579	CMK	blood:	n/a
10	chr5:14581529-14581579	SK-N-SH	brain:	n/a
11	chr5:14581529-14581579	ECC-1	luminal epithelium:	n/a
12	chr5:14581529-14581579	SAEC	small airway:	n/a
13	chr5:14581529-14581579	BE2_C	brain:	n/a
14	chr5:14581529-14581579	MCF-7	breast:	n/a
15	chr5:14581529-14581579	HRCEpiC	kidney:	n/a
16	chr5:14581529-14581579	SK-N-MC	brain:	n/a
17	chr5:14581529-14581579	HMEC	breast:	n/a
18	chr5:14581529-14581579	PFSK-1	brain:	n/a
19	chr5:14581529-14581579	NH-A	brain:	n/a
20	chr5:14581529-14581579	NHBE	bronchial:	n/a
21	chr5:14581529-14581579	AoSMC	blood vessel:	n/a
22	chr5:14581529-14581579	HUVEC	blood vessel:	n/a
23	chr5:14581529-14581579	HPAEpiC	pulmonary alveolar:	n/a
24	chr5:14581529-14581579	Hepatocyte	liver:	n/a
25	chr5:14581529-14581579	Jurkat	blood:	n/a
26	chr5:14581529-14581579	BJ	skin:	n/a
27	chr5:14581529-14581579	LNCaP	prostate:	n/a
28	chr5:14581529-14581579	MCF10A-Er-Src	breast:	n/a
29	chr5:14581529-14581579	HCF	heart:	n/a
30	chr5:14581529-14581579	T-47D	breast:	n/a
31	chr5:14581529-14581579	NB4	blood:	n/a
32	chr5:14581529-14581579	HCPEpiC	choroid plexus:	n/a
33	chr5:14581529-14581579	HCM	heart:	n/a
34	chr5:14581529-14581579	AG09309	skin:	n/a
35	chr5:14581529-14581579	HEK293	kidney:	embryo
36	chr5:14581529-14581579	AG09319	gingival:	n/a
37	chr5:14581529-14581579	HNPCEpiC	eye:	n/a
38	chr5:14581529-14581579	HRE	kidney:	n/a
39	chr5:14581529-14581579	GM12892	blood:	n/a
40	chr5:14581529-14581579	ovcar-3	ovarian:	n/a
41	chr5:14581529-14581579	U87	brain:	n/a
42	chr5:14581529-14581579	ProgFib	skin:	n/a
43	chr5:14581529-14581579	HL-60	blood:	n/a
44	chr5:14581529-14581579	RPTEC	kidney:	n/a
45	chr5:14581529-14581579	SKMC	muscle:	n/a
46	chr5:14581529-14581579	PANC-1	pancreas:	n/a
47	chr5:14581529-14581579	NT2-D1	testis:	n/a
48	chr5:14581529-14581579	HCT-116	colon:	n/a
49	chr5:14581529-14581579	HAEpiC	amniotic membrane:	n/a
50	chr5:14581529-14581579	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14487528..14489858-chr5:14581341..14583372,2	MCF-7	breast:
2	chr5:14497681..14499439-chr5:14580941..14582507,2	MCF-7	breast:

Variant related genes	Relation type
FAM105A	TF binding region
FAM105A	CpG island
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs152639	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs152641	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs152642	0.93[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs152643	0.93[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs152644	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv830211	chr5:14474675-14675776	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1032951	chr5:14529579-14667342	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv1796116	chr5:14572712-14582501	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv523575	chr5:14575698-14581556	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv1793651	chr5:14575698-14584695	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv1837962	chr5:14578546-14582501	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv1837207	chr5:14578799-14582501	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv597241	chr5:14581556-14582435	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
11	nsv597242	chr5:14581556-14582501	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
12	esv1839029	chr5:14581556-14584695	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
13	esv1837510	chr5:14581556-14591004	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs31978	GPAM	trans	cerebellum	SCAN
rs31978	FAM105A	cis	cerebellum	SCAN
rs31978	NAT10	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14580800-14581600	Enhancers	Fetal Brain Male	brain
2	chr5:14580800-14581600	Flanking Active TSS	Hela-S3	cervix
3	chr5:14580800-14581600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr5:14580800-14583400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr5:14580800-14583400	Active TSS	Colonic Mucosa	Colon
6	chr5:14581000-14581600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:14581000-14581600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr5:14581000-14581600	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr5:14581000-14583200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:14581000-14583400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:14581200-14581600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:14581200-14581600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr5:14581200-14581600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr5:14581200-14581600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr5:14581200-14581600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr5:14581200-14581600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr5:14581200-14581600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:14581200-14581600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr5:14581200-14581600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr5:14581200-14581600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:14581200-14581600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:14581200-14581600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr5:14581200-14581600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr5:14581200-14581600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr5:14581200-14581600	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
26	chr5:14581200-14581800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr5:14581200-14581800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:14581200-14581800	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr5:14581200-14581800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:14581200-14581800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr5:14581200-14581800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr5:14581200-14581800	Flanking Active TSS	Placenta	Placenta
33	chr5:14581200-14581800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
34	chr5:14581200-14582200	Active TSS	Stomach Smooth Muscle	stomach
35	chr5:14581200-14582600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:14581200-14582800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:14581200-14582800	Active TSS	Brain Hippocampus Middle	brain
38	chr5:14581200-14582800	Active TSS	Brain Substantia Nigra	brain
39	chr5:14581200-14582800	Active TSS	Right Atrium	heart
40	chr5:14581200-14583000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:14581200-14583000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr5:14581200-14583000	Bivalent/Poised TSS	NHEK	skin
43	chr5:14581200-14583200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr5:14581200-14583200	Active TSS	Brain Anterior Caudate	brain
45	chr5:14581200-14583200	Active TSS	Fetal Brain Female	brain
46	chr5:14581200-14583400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:14581200-14583400	Active TSS	Brain Angular Gyrus	brain
48	chr5:14581400-14581600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:14581400-14581600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:14581400-14581600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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