Variant report

Variant	rs7691817
Chromosome Location	chr4:54457861-54457862
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	PML	chr4:54457394-54458057	K562	blood:	n/a	n/a
2	CTCF	chr4:54457720-54457870	NHEK	skin:	n/a	chr4:54457829-54457845
3	POLR2A	chr4:54457435-54457943	ECC-1	luminal epithelium:	n/a	n/a
4	USF2	chr4:54457535-54458045	H1-hESC	embryonic stem cell:	n/a	n/a
5	TBP	chr4:54457469-54457976	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr4:54457443-54457933	K562	blood:	n/a	n/a
7	FOXA1	chr4:54457738-54457986	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr4:54457414-54458027	MCF-7	breast:	n/a	n/a
9	MAX	chr4:54457417-54458202	MCF-7	breast:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
10	EP300	chr4:54457550-54458412	K562	blood:	n/a	n/a
11	HCFC1	chr4:54457360-54457914	K562	blood:	n/a	n/a
12	ATF2	chr4:54457463-54457919	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr4:54457580-54457915	ECC-1	luminal epithelium:	n/a	chr4:54457726-54457739
14	MAX	chr4:54457480-54458089	K562	blood:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
15	POLR2A	chr4:54457354-54457962	MCF-7	breast:	n/a	n/a
16	GTF2F1	chr4:54457376-54457881	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr4:54457552-54458036	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr4:54457760-54457910	HMEC	breast:	n/a	chr4:54457829-54457845
19	MAX	chr4:54457405-54458121	K562	blood:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
20	POLR2A	chr4:54457219-54458066	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr4:54457753-54457942	LNCaP	prostate:	n/a	chr4:54457829-54457845
22	EP300	chr4:54457533-54458310	ECC-1	luminal epithelium:	n/a	n/a
23	JUND	chr4:54457476-54457912	H1-hESC	embryonic stem cell:	n/a	chr4:54457728-54457737
24	CREB1	chr4:54457557-54458009	ECC-1	luminal epithelium:	n/a	chr4:54457726-54457739
25	RAD21	chr4:54457531-54458094	MCF-7	breast:	n/a	n/a
26	TAF1	chr4:54457487-54457935	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr4:54457406-54458024	ECC-1	luminal epithelium:	n/a	n/a
28	SIN3AK20	chr4:54457477-54458003	H1-hESC	embryonic stem cell:	n/a	n/a
29	BHLHE40	chr4:54457269-54458103	K562	blood:	n/a	n/a
30	MAX	chr4:54457465-54458225	ECC-1	luminal epithelium:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
31	STAT3	chr4:54457739-54457931	MCF10A-Er-Src	breast:	n/a	n/a
32	TEAD4	chr4:54457541-54458085	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr4:54457734-54457965	MCF-7	breast:	n/a	chr4:54457829-54457845
34	MAX	chr4:54457470-54458014	H1-hESC	embryonic stem cell:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
35	FOXA1	chr4:54457640-54458061	T-47D	breast:	n/a	n/a
36	SIN3A	chr4:54457160-54458179	H1-hESC	embryonic stem cell:	n/a	n/a
37	USF1	chr4:54457705-54458074	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr4:54457497-54457867	ECC-1	luminal epithelium:	n/a	chr4:54457533-54457543
39	ELF1	chr4:54457349-54458142	MCF-7	breast:	n/a	chr4:54457713-54457726
40	CTCF	chr4:54457781-54457929	Kidney_OC	kidney:	n/a	chr4:54457829-54457845
41	ELF1	chr4:54457333-54458129	HCT-116	colon:	n/a	chr4:54457713-54457726
42	GATA3	chr4:54457525-54458053	T-47D	breast:	n/a	n/a
43	MYC	chr4:54457652-54458032	K562	blood:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
44	GATA3	chr4:54457501-54457992	T-47D	breast:	n/a	n/a
45	MYC	chr4:54457609-54457992	MCF-7	breast:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
46	NR3C1	chr4:54457693-54457998	ECC-1	luminal epithelium:	n/a	n/a
47	MAX	chr4:54457544-54458063	H1-hESC	embryonic stem cell:	n/a	chr4:54457911-54457922 chr4:54457912-54457922 chr4:54457794-54457804
48	CTCF	chr4:54457625-54458024	MCF-7	breast:	n/a	chr4:54457829-54457845
49	RAD21	chr4:54457515-54458083	ECC-1	luminal epithelium:	n/a	n/a
50	MAFK	chr4:54457245-54457898	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:54457842-54457892	HUVEC	blood vessel:	n/a
2	chr4:54457842-54457892	GM06990	blood:	n/a
3	chr4:54457842-54457892	Hela-S3	cervix:	n/a
4	chr4:54457842-54457892	AG04449	skin:	fetal
5	chr4:54457842-54457892	HEEpiC	esophagus:	n/a
6	chr4:54457842-54457892	AoSMC	blood vessel:	n/a
7	chr4:54457842-54457892	SK-N-SH_RA	brain:	n/a
8	chr4:54457842-54457892	RPTEC	kidney:	n/a
9	chr4:54457842-54457892	GM19239	blood:	n/a
10	chr4:54457842-54457892	HNPCEpiC	eye:	n/a
11	chr4:54457842-54457892	A549	lung:	n/a
12	chr4:54457842-54457892	HPAEpiC	pulmonary alveolar:	n/a
13	chr4:54457842-54457892	GM12891	blood:	n/a
14	chr4:54457842-54457892	HIPEpiC	eye:	n/a
15	chr4:54457842-54457892	AG09309	skin:	n/a
16	chr4:54457842-54457892	HepG2	liver:	n/a
17	chr4:54457842-54457892	SK-N-SH	brain:	n/a
18	chr4:54457842-54457892	AG10803	skin:	n/a
19	chr4:54457842-54457892	GM12892	blood:	n/a
20	chr4:54457842-54457892	HAEpiC	amniotic membrane:	n/a
21	chr4:54457842-54457892	HRPEpiC	eye:	n/a
22	chr4:54457842-54457892	HRCEpiC	kidney:	n/a
23	chr4:54457842-54457892	HL-60	blood:	n/a
24	chr4:54457842-54457892	MCF-7	breast:	n/a
25	chr4:54457842-54457892	ProgFib	skin:	n/a
26	chr4:54457842-54457892	NHDF-neo	bronchial:	n/a
27	chr4:54457842-54457892	HCF	heart:	n/a
28	chr4:54457842-54457892	BJ	skin:	n/a
29	chr4:54457842-54457892	GM12878	blood:	n/a
30	chr4:54457842-54457892	HEK293	kidney:	embryo
31	chr4:54457842-54457892	BE2_C	brain:	n/a
32	chr4:54457842-54457892	PFSK-1	brain:	n/a
33	chr4:54457842-54457892	T-47D	breast:	n/a
34	chr4:54457842-54457892	ovcar-3	ovarian:	n/a
35	chr4:54457842-54457892	Caco-2	colon:	n/a
36	chr4:54457842-54457892	Hepatocyte	liver:	n/a
37	chr4:54457842-54457892	MCF10A-Er-Src	breast:	n/a
38	chr4:54457842-54457892	K562	blood:	n/a
39	chr4:54457842-54457892	HMEC	breast:	n/a
40	chr4:54457842-54457892	IMR90	lung:	fetal
41	chr4:54457842-54457892	HCPEpiC	choroid plexus:	n/a
42	chr4:54457842-54457892	SK-N-MC	brain:	n/a
43	chr4:54457842-54457892	NH-A	brain:	n/a
44	chr4:54457842-54457892	HCM	heart:	n/a
45	chr4:54457842-54457892	HRE	kidney:	n/a
46	chr4:54457842-54457892	LNCaP	prostate:	n/a
47	chr4:54457842-54457892	PrEC	prostate:	n/a
48	chr4:54457842-54457892	PANC-1	pancreas:	n/a
49	chr4:54457842-54457892	HCT-116	colon:	n/a
50	chr4:54457842-54457892	SAEC	small airway:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:53577014..53579334-chr4:54455969..54458582,2	K562	blood:
2	chr4:54441539..54444052-chr4:54456319..54458612,3	MCF-7	breast:
3	chr4:54441243..54444280-chr4:54454649..54458129,3	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region
LNX1-AS2	TF binding region
LNX1	CpG island
LNX1-AS2	CpG island
ENSG00000226950	Chromatin interaction
ENSG00000173966	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10517304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10517305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11936500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11942048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11945338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12186283	0.94[YRI][hapmap]
rs17083112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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];0.95[ASN][1000 genomes]
rs2099452	0.94[CEU][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv437918	chr4:54451175-54483569	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879014	chr4:54451246-54461548	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7691817	LNX1	cis	lymphoblastoid	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54452600-54458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:54452600-54459600	Enhancers	HepG2	liver
3	chr4:54452800-54458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:54452800-54459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:54453000-54458800	Weak transcription	Small Intestine	intestine
6	chr4:54453200-54459200	Weak transcription	Osteobl	bone
7	chr4:54454200-54458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:54454600-54459000	Enhancers	Fetal Muscle Leg	muscle
9	chr4:54454800-54459000	Weak transcription	Aorta	Aorta
10	chr4:54455400-54458400	Weak transcription	Left Ventricle	heart
11	chr4:54455600-54458000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr4:54455800-54458000	Active TSS	Fetal Kidney	kidney
13	chr4:54455800-54458200	Weak transcription	Fetal Heart	heart
14	chr4:54455800-54459000	Enhancers	Adipose Nuclei	Adipose
15	chr4:54456000-54458200	Active TSS	Duodenum Mucosa	Duodenum
16	chr4:54456000-54458200	Active TSS	Pancreas	Pancrea
17	chr4:54456000-54460000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:54456200-54458000	Active TSS	Fetal Intestine Large	intestine
19	chr4:54456200-54458200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:54456200-54458600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:54456400-54458000	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:54456400-54458200	Active TSS	Stomach Mucosa	stomach
23	chr4:54456600-54458000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr4:54456600-54458000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:54456800-54458000	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr4:54456800-54458000	Active TSS	Fetal Intestine Small	intestine
27	chr4:54456800-54458600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:54456800-54459000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr4:54457000-54458200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr4:54457000-54458400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr4:54457000-54459000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:54457000-54459200	Enhancers	Fetal Lung	lung
33	chr4:54457200-54458000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr4:54457200-54460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr4:54457400-54458000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:54457400-54458200	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr4:54457400-54458400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr4:54457400-54459000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr4:54457400-54459000	Enhancers	Fetal Muscle Trunk	muscle
40	chr4:54457400-54459000	Enhancers	Right Atrium	heart
41	chr4:54457400-54459600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:54457400-54459800	Flanking Active TSS	NHEK	skin
43	chr4:54457600-54458000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:54457600-54458000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:54457600-54458000	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr4:54457600-54458000	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr4:54457600-54458000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr4:54457600-54458000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr4:54457600-54458000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr4:54457600-54458000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--

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