Variant report

Variant	rs8106495
Chromosome Location	chr19:36394678-36394679
allele	C/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	NRF1	chr19:36394576-36394995	SK-N-SH	brain:	n/a	chr19:36394775-36394786
2	BHLHE40	chr19:36394575-36394865	K562	blood:	n/a	n/a
3	MAX	chr19:36394530-36394997	A549	lung:	n/a	chr19:36394574-36394584
4	GABPA	chr19:36394511-36394853	GM12878	blood:	n/a	n/a
5	CHD1	chr19:36394422-36394851	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:36394386-36394867	K562	blood:	n/a	n/a
7	ELF1	chr19:36394479-36394880	K562	blood:	n/a	n/a
8	POLR2A	chr19:36394396-36394936	GM12878	blood:	n/a	n/a
9	GABPA	chr19:36394455-36394890	K562	blood:	n/a	n/a
10	CREB1	chr19:36394367-36395143	GM12878	blood:	n/a	n/a
11	PAX5	chr19:36394254-36395261	GM12878	blood:	n/a	chr19:36394591-36394600
12	POLR2A	chr19:36394343-36394885	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFATC1	chr19:36394432-36395164	GM12878	blood:	n/a	n/a
14	IKZF1	chr19:36394186-36394870	GM12878	blood:	n/a	n/a
15	MAX	chr19:36394474-36395027	GM12878	blood:	n/a	chr19:36394574-36394584
16	RELA	chr19:36394443-36395246	GM19193	blood:	n/a	n/a
17	POLR2A	chr19:36394598-36394862	Gliobla	brain:	n/a	n/a
18	HDAC2	chr19:36394547-36394869	K562	blood:	n/a	n/a
19	NFIC	chr19:36394376-36395183	GM12878	blood:	n/a	n/a
20	SIN3A	chr19:36394489-36395073	GM12878	blood:	n/a	n/a
21	MEF2A	chr19:36394469-36394996	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:36394441-36394847	SK-N-MC	brain:	n/a	n/a
23	ATF2	chr19:36394462-36395037	GM12878	blood:	n/a	n/a
24	ZNF143	chr19:36394636-36394836	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr19:36394482-36394903	H1-hESC	embryonic stem cell:	n/a	n/a
26	CBX3	chr19:36394461-36394888	K562	blood:	n/a	n/a
27	ELK1	chr19:36394313-36395039	GM12878	blood:	n/a	n/a
28	GABPA	chr19:36394534-36394810	GM12878	blood:	n/a	n/a
29	MYC	chr19:36394495-36394931	K562	blood:	n/a	chr19:36394574-36394584
30	EBF1	chr19:36394418-36395217	GM12878	blood:	n/a	chr19:36394961-36394971 chr19:36394885-36394896 chr19:36394962-36394971 chr19:36394960-36394973 chr19:36394844-36394855 chr19:36394873-36394884 chr19:36394962-36394971
31	PAX5	chr19:36394504-36395146	GM12878	blood:	n/a	chr19:36394591-36394600
32	TBL1XR1	chr19:36394473-36394820	K562	blood:	n/a	n/a
33	EP300	chr19:36394408-36395041	GM12878	blood:	n/a	n/a
34	PML	chr19:36394503-36394838	K562	blood:	n/a	n/a
35	ELF1	chr19:36394421-36395009	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:36394200-36394898	GM19193	blood:	n/a	n/a
37	POU2F2	chr19:36394576-36394952	GM12878	blood:	n/a	n/a
38	EP300	chr19:36394502-36395094	GM12878	blood:	n/a	n/a
39	HMGN3	chr19:36394421-36394892	K562	blood:	n/a	n/a
40	GABPA	chr19:36394547-36394826	HepG2	liver:	n/a	n/a
41	ELF1	chr19:36394400-36394976	MCF-7	breast:	n/a	n/a
42	CTCF	chr19:36394660-36394810	MCF-7	breast:	n/a	n/a
43	POLR2A	chr19:36394142-36394860	GM12892	blood:	n/a	n/a
44	GABPA	chr19:36394299-36394976	K562	blood:	n/a	n/a
45	TCF12	chr19:36394587-36395064	GM12878	blood:	n/a	n/a
46	SIN3AK20	chr19:36394355-36394764	H1-hESC	embryonic stem cell:	n/a	n/a
47	EGR1	chr19:36394498-36394999	H1-hESC	embryonic stem cell:	n/a	chr19:36394755-36394769 chr19:36394574-36394587 chr19:36394573-36394588 chr19:36394574-36394587 chr19:36394776-36394790
48	TEAD4	chr19:36394499-36394938	K562	blood:	n/a	n/a
49	YY1	chr19:36394434-36394903	K562	blood:	n/a	n/a
50	MAZ	chr19:36394525-36394867	HepG2	liver:	n/a	chr19:36394574-36394584

No.	Distal block	Cell Line	Cell type
1	chr19:36387478..36389349-chr19:36394132..36396571,2	MCF-7	breast:
2	chr19:36359598..36361922-chr19:36393124..36395167,2	K562	blood:
3	chr19:36389776..36392991-chr19:36393581..36401271,10	K562	blood:
4	chr19:36205479..36207948-chr19:36393989..36396293,2	K562	blood:
5	chr19:36393311..36395845-chr19:36427548..36429396,2	MCF-7	breast:
6	chr19:36393181..36395162-chr19:36544398..36547293,2	K562	blood:
7	chr19:36390133..36392611-chr19:36392789..36396319,5	MCF-7	breast:

Variant related genes	Relation type
NFKBID	TF binding region
ENSG00000167604	Chromatin interaction
ENSG00000105290	Chromatin interaction
ENSG00000126243	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000161277	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11878547	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880785	1.00[MEX][hapmap]
rs1268319	1.00[MEX][hapmap]
rs16960862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17173033	0.83[ASN][1000 genomes]
rs17549166	0.83[EUR][1000 genomes]
rs1802029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];1.00[ASN][1000 genomes]
rs230260	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs230261	1.00[MEX][hapmap]
rs33964243	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761086	1.00[CEU][hapmap]
rs376240	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs56264349	0.83[ASN][1000 genomes]
rs58422001	0.91[ASN][1000 genomes]
rs7245383	1.00[CEU][hapmap]
rs7247769	1.00[CEU][hapmap]
rs7251744	0.90[ASN][1000 genomes]
rs7251879	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7252902	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253040	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256952	1.00[CEU][hapmap]
rs7258154	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258214	0.90[ASN][1000 genomes]
rs7258909	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8101472	1.00[CEU][hapmap]
rs8103718	1.00[CEU][hapmap]
rs8105153	0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108360	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8108459	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111740	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113704	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs879407	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[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
rs8106495	LRFN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36390800-36395400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:36391000-36395000	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr19:36391600-36395000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:36391600-36395000	Flanking Active TSS	Fetal Thymus	thymus
5	chr19:36391600-36395000	Enhancers	Spleen	Spleen
6	chr19:36391600-36397400	Weak transcription	Stomach Mucosa	stomach
7	chr19:36391800-36395000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr19:36391800-36395000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:36391800-36395200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr19:36391800-36395200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr19:36391800-36395200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr19:36391800-36395200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr19:36391800-36395200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr19:36391800-36396000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr19:36391800-36396000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:36391800-36396400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:36392000-36394800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:36392000-36394800	Enhancers	NHDF-Ad	bronchial
19	chr19:36392000-36395200	Flanking Active TSS	GM12878-XiMat	blood
20	chr19:36392000-36398000	Weak transcription	Brain Angular Gyrus	brain
21	chr19:36392200-36397400	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:36392200-36398600	Weak transcription	Right Atrium	heart
23	chr19:36392600-36394800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:36392600-36394800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:36392600-36395000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:36392800-36394800	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:36392800-36394800	Active TSS	Rectal Smooth Muscle	rectum
28	chr19:36393200-36395000	Enhancers	Lung	lung
29	chr19:36393400-36394800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:36393400-36394800	Active TSS	Duodenum Mucosa	Duodenum
31	chr19:36393600-36397400	Weak transcription	Hela-S3	cervix
32	chr19:36393800-36394800	Flanking Active TSS	Placenta	Placenta
33	chr19:36394000-36394800	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:36394000-36394800	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr19:36394000-36394800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:36394000-36394800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr19:36394000-36394800	Active TSS	Stomach Smooth Muscle	stomach
38	chr19:36394000-36394800	Active TSS	Thymus	Thymus
39	chr19:36394000-36395000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:36394000-36395000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:36394000-36395200	Flanking Active TSS	Dnd41	blood
42	chr19:36394000-36398000	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:36394200-36394800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr19:36394200-36394800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:36394200-36394800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:36394200-36394800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr19:36394200-36394800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:36394200-36394800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:36394200-36394800	Active TSS	Brain Anterior Caudate	brain
50	chr19:36394200-36394800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine

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