Variant report

Variant	rs909136
Chromosome Location	chr19:36422706-36422707
allele	A/C
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	chr19:36422136-36422777	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr19:36422640-36422790	GM12871	blood:	n/a	chr19:36422697-36422710
3	CTCF	chr19:36422600-36422750	HUVEC	blood vessel:	n/a	chr19:36422697-36422710
4	ETS1	chr19:36422400-36422760	K562	blood:	n/a	chr19:36422593-36422606 chr19:36422594-36422607
5	ZBTB33	chr19:36422477-36422775	HepG2	liver:	n/a	chr19:36422636-36422651
6	JUN	chr19:36422338-36422853	K562	blood:	n/a	n/a
7	CTCF	chr19:36422680-36422830	WI-38	lung:	n/a	chr19:36422697-36422710
8	POLR2A	chr19:36422119-36422782	GM15510	blood:	n/a	n/a
9	ZMIZ1	chr19:36422197-36422832	K562	blood:	n/a	n/a
10	CTCF	chr19:36422640-36422790	AG04449	skin:	n/a	chr19:36422697-36422710
11	MAZ	chr19:36422011-36423028	IMR90	lung:	n/a	chr19:36422407-36422416 chr19:36422406-36422416 chr19:36422406-36422417 chr19:36422403-36422418 chr19:36422408-36422415
12	ELK4	chr19:36422312-36422775	HEK293	kidney:	n/a	n/a
13	PML	chr19:36421935-36422913	GM12878	blood:	n/a	chr19:36422347-36422355
14	CREB1	chr19:36422173-36422898	ECC-1	luminal epithelium:	n/a	n/a
15	E2F1	chr19:36422258-36422763	Hela-S3	cervix:	n/a	chr19:36422444-36422453
16	E2F6	chr19:36422249-36422824	K562	blood:	n/a	chr19:36422444-36422453
17	TEAD4	chr19:36422430-36422921	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:36422600-36422820	HepG2	liver:	n/a	chr19:36422697-36422710
19	CTCF	chr19:36422285-36423081	GM12878	blood:	n/a	chr19:36422697-36422710
20	RELA	chr19:36422278-36422900	GM19193	blood:	n/a	n/a
21	CTCF	chr19:36422531-36423058	GM12892	blood:	n/a	chr19:36422697-36422710
22	CTCF	chr19:36422600-36422750	HCFaa	heart:	n/a	chr19:36422697-36422710
23	SIX5	chr19:36422363-36422777	H1-hESC	embryonic stem cell:	n/a	chr19:36422594-36422603 chr19:36422596-36422605 chr19:36422593-36422607
24	RCOR1	chr19:36422161-36423061	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr19:36422461-36423057	IMR90	lung:	n/a	chr19:36422697-36422710
26	STAT3	chr19:36422333-36422760	MCF10A-Er-Src	breast:	n/a	chr19:36422590-36422598 chr19:36422588-36422599
27	MAFK	chr19:36422330-36422998	K562	blood:	n/a	n/a
28	IRF1	chr19:36422230-36422807	K562	blood:	n/a	chr19:36422530-36422544 chr19:36422762-36422776
29	CTCF	chr19:36422535-36422871	GM12891	blood:	n/a	chr19:36422697-36422710
30	CREB1	chr19:36422164-36422917	K562	blood:	n/a	n/a
31	CCNT2	chr19:36422239-36422829	K562	blood:	n/a	chr19:36422763-36422772
32	YY1	chr19:36422198-36422829	H1-hESC	embryonic stem cell:	n/a	chr19:36422666-36422680 chr19:36422665-36422679
33	MXI1	chr19:36422226-36422837	Hela-S3	cervix:	n/a	chr19:36422703-36422712 chr19:36422406-36422415 chr19:36422794-36422809 chr19:36422792-36422807
34	YY1	chr19:36422317-36422780	K562	blood:	n/a	chr19:36422666-36422680 chr19:36422665-36422679
35	GABPA	chr19:36422337-36422777	HepG2	liver:	n/a	chr19:36422443-36422454 chr19:36422667-36422676 chr19:36422445-36422454 chr19:36422440-36422454 chr19:36422443-36422457 chr19:36422665-36422674
36	SRF	chr19:36422179-36422919	MCF-7	breast:	n/a	n/a
37	ZNF384	chr19:36422210-36422810	K562	blood:	n/a	n/a
38	POLR2A	chr19:36422125-36422886	H1-neurons	neurons:	n/a	n/a
39	YY1	chr19:36422146-36422861	GM12892	blood:	n/a	chr19:36422666-36422680 chr19:36422665-36422679
40	ZBTB33	chr19:36422161-36422905	SK-N-SH	brain:	n/a	chr19:36422636-36422651
41	ZBTB33	chr19:36422331-36422898	GM12878	blood:	n/a	chr19:36422636-36422651
42	REST	chr19:36422159-36422881	PFSK-1	brain:	n/a	chr19:36422425-36422438
43	CTCF	chr19:36422600-36422750	HepG2	liver:	n/a	chr19:36422697-36422710
44	STAT5A	chr19:36422037-36423140	GM12878	blood:	n/a	chr19:36422590-36422598
45	USF1	chr19:36422187-36422882	SK-N-SH_RA	brain:	n/a	chr19:36422665-36422681
46	RAD21	chr19:36421765-36423179	A549	lung:	n/a	chr19:36422700-36422714 chr19:36422919-36422932
47	HMGN3	chr19:36422255-36422801	K562	blood:	n/a	n/a
48	SIX5	chr19:36422421-36422849	K562	blood:	n/a	chr19:36422594-36422603 chr19:36422596-36422605 chr19:36422593-36422607
49	MYC	chr19:36422208-36422863	K562	blood:	n/a	chr19:36422407-36422416 chr19:36422406-36422416 chr19:36422406-36422417 chr19:36422403-36422418 chr19:36422408-36422415
50	WRNIP1	chr19:36422136-36422908	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36373153..36373654-chr19:36422341..36423119,2	MCF-7	breast:
2	chr19:36230402..36233107-chr19:36420998..36423938,3	K562	blood:
3	chr19:36388372..36393126-chr19:36420797..36424227,6	MCF-7	breast:
4	chr19:36421247..36424179-chr19:36438110..36439999,2	MCF-7	breast:
5	chr19:36422429..36424100-chr19:36425397..36427908,2	MCF-7	breast:
6	chr19:36207964..36208549-chr19:36422265..36423107,3	MCF-7	breast:
7	chr19:36372649..36373645-chr19:36422216..36423598,12	MCF-7	breast:
8	chr19:36422201..36422822-chr3:136471199..136471915,2	HCT-116	colon:
9	chr19:36393312..36396233-chr19:36420925..36423547,3	K562	blood:
10	chr15:65597032..65597731-chr19:36422199..36422749,2	HCT-116	colon:
11	chr19:36207421..36208896-chr19:36422255..36423160,8	K562	blood:
12	chr19:36184355..36185390-chr19:36422209..36423187,11	K562	blood:
13	chr19:36372265..36373696-chr19:36422223..36423187,14	K562	blood:
14	chr19:36370591..36373174-chr19:36422249..36423786,2	MCF-7	breast:
15	chr19:36359450..36361367-chr19:36421125..36423142,2	K562	blood:
16	chr19:36390886..36393045-chr19:36420979..36424222,3	K562	blood:
17	chr19:36415212..36417969-chr19:36419526..36423356,3	MCF-7	breast:
18	chr19:36184393..36185382-chr19:36422317..36423468,4	MCF-7	breast:

Variant related genes	Relation type
LRFN3	TF binding region
ENSG00000126243	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000105290	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000126264	Chromatin interaction
ENSG00000167604	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10221461	0.85[ASN][1000 genomes]
rs10221486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057265	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11878444	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878880	0.93[ASN][1000 genomes]
rs11879537	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880835	0.93[ASN][1000 genomes]
rs11880859	0.93[ASN][1000 genomes]
rs11881157	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883234	0.91[ASN][1000 genomes]
rs13382036	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242590	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293756	0.93[ASN][1000 genomes]
rs34933126	0.95[EUR][1000 genomes]
rs55686886	0.93[ASN][1000 genomes]
rs56042927	0.93[ASN][1000 genomes]
rs56132631	0.83[ASN][1000 genomes]
rs56132838	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56187901	0.93[ASN][1000 genomes]
rs56230692	0.93[ASN][1000 genomes]
rs56744930	0.95[EUR][1000 genomes]
rs56922307	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57068163	0.86[EUR][1000 genomes]
rs57094555	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57412339	0.81[EUR][1000 genomes]
rs57516855	0.90[EUR][1000 genomes]
rs57785375	0.93[ASN][1000 genomes]
rs57962062	0.82[EUR][1000 genomes]
rs58161969	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58456578	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58504183	0.90[EUR][1000 genomes]
rs58551711	0.90[EUR][1000 genomes]
rs58768499	0.90[ASN][1000 genomes]
rs58976020	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59150589	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59151712	0.93[ASN][1000 genomes]
rs59399698	0.90[EUR][1000 genomes]
rs59416903	0.82[EUR][1000 genomes]
rs59478831	0.85[EUR][1000 genomes]
rs59534183	0.90[EUR][1000 genomes]
rs60073802	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60276253	0.93[ASN][1000 genomes]
rs60500471	0.93[ASN][1000 genomes]
rs60892678	0.93[ASN][1000 genomes]
rs60935148	0.90[EUR][1000 genomes]
rs61510077	0.88[ASN][1000 genomes]
rs61660311	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61672461	0.95[EUR][1000 genomes]
rs7245383	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7246259	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247246	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7247769	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7248253	0.93[ASN][1000 genomes]
rs7248265	0.93[ASN][1000 genomes]
rs7249502	0.93[ASN][1000 genomes]
rs7249567	0.92[CHB][hapmap]
rs7251380	0.93[ASN][1000 genomes]
rs7251422	0.85[ASN][1000 genomes]
rs7252053	0.85[ASN][1000 genomes]
rs7252526	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252572	0.90[ASN][1000 genomes]
rs7252693	0.93[ASN][1000 genomes]
rs7252839	0.93[ASN][1000 genomes]
rs7253086	0.90[EUR][1000 genomes]
rs7254298	0.93[ASN][1000 genomes]
rs7254335	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254905	0.93[ASN][1000 genomes]
rs7254994	0.93[ASN][1000 genomes]
rs7255824	0.93[ASN][1000 genomes]
rs7256280	0.95[EUR][1000 genomes]
rs7256433	0.90[EUR][1000 genomes]
rs7256952	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7257789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257911	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259892	0.93[ASN][1000 genomes]
rs7260613	0.85[EUR][1000 genomes]
rs73590883	0.85[EUR][1000 genomes]
rs73590895	0.81[EUR][1000 genomes]
rs73599539	0.86[EUR][1000 genomes]
rs73599540	0.86[EUR][1000 genomes]
rs73599546	0.86[EUR][1000 genomes]
rs73599554	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599561	0.95[EUR][1000 genomes]
rs73599565	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599577	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599586	0.95[EUR][1000 genomes]
rs73599600	0.90[EUR][1000 genomes]
rs73599602	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73928364	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73928368	0.93[ASN][1000 genomes]
rs73928369	0.93[ASN][1000 genomes]
rs8110868	0.86[EUR][1000 genomes]
rs909135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs909136	LRFN3	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36420400-36423000	Enhancers	Fetal Thymus	thymus
2	chr19:36420800-36423000	Enhancers	Spleen	Spleen
3	chr19:36421200-36423200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:36421600-36422800	Active TSS	Thymus	Thymus
5	chr19:36421800-36422800	Active TSS	Brain Anterior Caudate	brain
6	chr19:36421800-36422800	Enhancers	Fetal Heart	heart
7	chr19:36422000-36422800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:36422000-36422800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:36422000-36422800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:36422000-36422800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:36422000-36422800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:36422000-36422800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:36422000-36422800	Active TSS	Brain Angular Gyrus	brain
14	chr19:36422000-36422800	Active TSS	Brain Cingulate Gyrus	brain
15	chr19:36422000-36422800	Active TSS	Brain Germinal Matrix	brain
16	chr19:36422000-36422800	Active TSS	Brain Hippocampus Middle	brain
17	chr19:36422000-36422800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:36422000-36422800	Active TSS	Brain Substantia Nigra	brain
19	chr19:36422000-36423000	Active TSS	Psoas Muscle	Psoas
20	chr19:36422000-36423200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:36422000-36423200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr19:36422000-36423200	Enhancers	Placenta	Placenta
23	chr19:36422000-36423400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr19:36422200-36422800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:36422200-36422800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr19:36422200-36422800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36422200-36422800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:36422200-36422800	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr19:36422200-36422800	Active TSS	A549	lung
30	chr19:36422200-36423000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:36422200-36423000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:36422200-36423000	Active TSS	K562	blood
33	chr19:36422200-36423200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:36422200-36423400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr19:36422200-36426600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr19:36422400-36422800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:36422400-36422800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:36422400-36422800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:36422400-36422800	Enhancers	Rectal Smooth Muscle	rectum
40	chr19:36422400-36422800	Genic enhancers	Right Atrium	heart
41	chr19:36422400-36422800	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:36422400-36422800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr19:36422400-36422800	Enhancers	Stomach Smooth Muscle	stomach
44	chr19:36422400-36422800	Active TSS	Dnd41	blood
45	chr19:36422400-36423000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:36422400-36423000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:36422400-36423000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr19:36422400-36423000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr19:36422400-36423000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr19:36422400-36423000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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