Variant report

Variant	rs1111179
Chromosome Location	chr14:42075952-42075953
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	MAX	chr14:42075914-42076462	HepG2	liver:	n/a	n/a
2	EGR1	chr14:42075575-42076100	H1-hESC	embryonic stem cell:	n/a	chr14:42075857-42075870 chr14:42075858-42075867 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075871 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075870
3	EGR1	chr14:42075610-42076069	H1-hESC	embryonic stem cell:	n/a	chr14:42075857-42075870 chr14:42075858-42075867 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075871 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075870
4	MXI1	chr14:42074259-42076033	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr14:42075651-42076689	IMR90	lung:	n/a	n/a
6	EGR1	chr14:42075693-42075977	K562	blood:	n/a	chr14:42075857-42075870 chr14:42075858-42075867 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075871 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075870
7	POLR2A	chr14:42074981-42076018	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr14:42073356-42076621	SK-N-MC	brain:	n/a	n/a
9	MAX	chr14:42075930-42076556	MCF-7	breast:	n/a	n/a
10	BACH1	chr14:42075723-42076570	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr14:42073598-42077869	H1-hESC	embryonic stem cell:	n/a	chr14:42077621-42077630 chr14:42076170-42076179 chr14:42075971-42075982
12	CTBP2	chr14:42074050-42077848	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr14:42075006-42076058	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr14:42075624-42077921	H1-neurons	neurons:	n/a	n/a
15	TAF1	chr14:42075792-42076098	H1-hESC	embryonic stem cell:	n/a	n/a
16	TCF7L2	chr14:42075777-42075956	PANC-1	pancreas:	n/a	n/a
17	SP1	chr14:42075558-42075994	H1-hESC	embryonic stem cell:	n/a	chr14:42075839-42075853
18	SP1	chr14:42074961-42075964	H1-hESC	embryonic stem cell:	n/a	chr14:42075839-42075853
19	MAX	chr14:42075923-42076427	ECC-1	luminal epithelium:	n/a	n/a
20	REST	chr14:42074960-42077937	H1-neurons	neurons:	n/a	chr14:42077585-42077598 chr14:42076936-42076956 chr14:42076170-42076180 chr14:42077503-42077513 chr14:42076268-42076278 chr14:42075096-42075104 chr14:42077314-42077327 chr14:42076038-42076056
21	SIN3AK20	chr14:42075727-42076055	H1-hESC	embryonic stem cell:	n/a	n/a
22	EGR1	chr14:42075680-42076037	ECC-1	luminal epithelium:	n/a	chr14:42075857-42075870 chr14:42075858-42075867 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075871 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075870
23	POLR2A	chr14:42075888-42075992	MCF-7	breast:	n/a	n/a
24	POLR2A	chr14:42075639-42077939	H1-neurons	neurons:	n/a	n/a
25	ZNF143	chr14:42075765-42076446	H1-hESC	embryonic stem cell:	n/a	chr14:42075852-42075870
26	MAX	chr14:42075951-42076525	A549	lung:	n/a	n/a
27	JUND	chr14:42075688-42075959	H1-hESC	embryonic stem cell:	n/a	chr14:42075816-42075830
28	MAX	chr14:42075848-42076587	HepG2	liver:	n/a	n/a
29	EGR1	chr14:42075623-42076068	MCF-7	breast:	n/a	chr14:42075857-42075870 chr14:42075858-42075867 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075871 chr14:42075858-42075868 chr14:42075857-42075870 chr14:42075856-42075870
30	JUN	chr14:42075818-42075975	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LRFN5	TF binding region
ENSG00000258636	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10131184	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10140527	0.96[CEU][hapmap];0.96[TSI][hapmap]
rs10483526	0.91[EUR][1000 genomes]
rs1111177	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11157240	0.84[EUR][1000 genomes]
rs11157241	0.89[EUR][1000 genomes]
rs11157242	0.83[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1117723	0.83[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1137567	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12100476	0.85[JPT][hapmap]
rs12100840	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12100891	0.85[JPT][hapmap]
rs12431444	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12589043	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12589112	0.83[ASN][1000 genomes]
rs1609735	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17112133	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17112137	0.83[ASN][1000 genomes]
rs17781288	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1950831	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1950834	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1950835	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1950836	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1950838	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1956446	0.85[JPT][hapmap]
rs1956447	0.85[JPT][hapmap]
rs1956450	0.91[EUR][1000 genomes]
rs1998126	0.83[ASN][1000 genomes]
rs2121708	0.83[EUR][1000 genomes]
rs28755010	0.86[ASN][1000 genomes]
rs2899928	0.83[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4356390	0.95[EUR][1000 genomes]
rs58845274	0.83[ASN][1000 genomes]
rs61990286	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61990288	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61990289	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6572099	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7148091	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72684563	0.89[EUR][1000 genomes]
rs8003822	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8007172	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8013655	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][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	nsv1047300	chr14:41671653-42361098	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831164	chr14:41673017-42103168	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv533968	chr14:41882101-42327882	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1042078	chr14:41993985-42120143	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758353	chr14:42045873-42259511	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2759983	chr14:42045873-42259511	ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	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
rs1111179	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:42070200-42076800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:42070800-42077000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:42071000-42076200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr14:42071400-42076200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr14:42071400-42079800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr14:42072000-42078000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr14:42072200-42076400	Active TSS	Fetal Lung	lung
8	chr14:42072800-42077000	Active TSS	Fetal Kidney	kidney
9	chr14:42073000-42076200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr14:42073000-42076600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:42073000-42077200	Active TSS	Ovary	ovary
12	chr14:42073000-42079600	Active TSS	Right Atrium	heart
13	chr14:42073200-42076400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr14:42073200-42076800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:42073400-42076200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:42073400-42076400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:42073400-42076400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr14:42073400-42076400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr14:42073400-42076400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
20	chr14:42073400-42076800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr14:42073600-42078400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
22	chr14:42073600-42079800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
23	chr14:42073800-42076800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:42073800-42076800	Bivalent/Poised TSS	Osteobl	bone
25	chr14:42073800-42077600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
26	chr14:42073800-42077800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr14:42073800-42077800	Bivalent/Poised TSS	Left Ventricle	heart
28	chr14:42074000-42077400	Bivalent/Poised TSS	Fetal Thymus	thymus
29	chr14:42074000-42077800	Bivalent/Poised TSS	Psoas Muscle	Psoas
30	chr14:42074000-42078200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
31	chr14:42074200-42076000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr14:42074200-42076000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr14:42074200-42076400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr14:42074200-42076600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:42074200-42076800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:42074200-42077600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr14:42074400-42077800	Bivalent/Poised TSS	NHLF	lung
38	chr14:42074600-42076000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
39	chr14:42074600-42076000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
40	chr14:42074600-42076600	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr14:42074800-42076600	Bivalent/Poised TSS	Colonic Mucosa	Colon
42	chr14:42074800-42077800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
43	chr14:42074800-42079800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:42075000-42076000	Enhancers	Gastric	stomach
45	chr14:42075000-42076400	Enhancers	Spleen	Spleen
46	chr14:42075000-42078200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr14:42075200-42076000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr14:42075200-42076000	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr14:42075200-42076000	Active TSS	Pancreas	Pancrea
50	chr14:42075200-42076200	Active TSS	Right Ventricle	heart

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