Variant report

Variant	rs246143
Chromosome Location	chr16:69458369-69458370
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	TBP	chr16:69458039-69458980	GM12878	blood:	n/a	n/a
2	SP1	chr16:69457898-69459315	A549	lung:	n/a	chr16:69458388-69458399 chr16:69458291-69458312
3	YY1	chr16:69458097-69458984	SK-N-SH	brain:	n/a	n/a
4	CBX3	chr16:69457934-69458680	K562	blood:	n/a	n/a
5	POU2F2	chr16:69458090-69459025	GM12891	blood:	n/a	n/a
6	ZBTB33	chr16:69458276-69458809	A549	lung:	n/a	chr16:69458308-69458315
7	ELF1	chr16:69458001-69458944	A549	lung:	n/a	n/a
8	EP300	chr16:69458348-69458750	GM12878	blood:	n/a	chr16:69458382-69458395
9	POLR2A	chr16:69458076-69458849	K562	blood:	n/a	n/a
10	NFYB	chr16:69458060-69458722	K562	blood:	n/a	chr16:69458461-69458471 chr16:69458298-69458313 chr16:69458333-69458346 chr16:69458301-69458311 chr16:69458299-69458313 chr16:69458418-69458433 chr16:69458298-69458313
11	POLR2A	chr16:69457983-69459316	GM12878	blood:	n/a	n/a
12	RFX5	chr16:69458056-69459145	Hela-S3	cervix:	n/a	chr16:69458471-69458480 chr16:69458461-69458470 chr16:69458467-69458482 chr16:69458470-69458484
13	TAF1	chr16:69458089-69458912	SK-N-SH	brain:	n/a	n/a
14	RCOR1	chr16:69458000-69458703	HepG2	liver:	n/a	n/a
15	GTF2F1	chr16:69458148-69458752	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr16:69458025-69459368	GM12878	blood:	n/a	n/a
17	YY1	chr16:69458325-69458820	H1-hESC	embryonic stem cell:	n/a	n/a
18	HNF4A	chr16:69458202-69458608	HepG2	liver:	n/a	n/a
19	TBL1XR1	chr16:69458211-69458705	K562	blood:	n/a	n/a
20	POLR2A	chr16:69458026-69459159	GM19193	blood:	n/a	n/a
21	POLR2A	chr16:69457955-69458890	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr16:69458309-69459257	Hela-S3	cervix:	n/a	n/a
23	EGR1	chr16:69458208-69458674	K562	blood:	n/a	chr16:69458383-69458398 chr16:69458385-69458396 chr16:69458380-69458402 chr16:69458384-69458397
24	SREBP2	chr16:69457722-69460132	GM12878	blood:	n/a	n/a
25	TBP	chr16:69458105-69459277	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr16:69458117-69458894	GM12878	blood:	n/a	n/a
27	CHD2	chr16:69458086-69459022	K562	blood:	n/a	chr16:69458797-69458807 chr16:69458379-69458389
28	MXI1	chr16:69458048-69458798	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr16:69458146-69458814	K562	blood:	n/a	chr16:69458300-69458309 chr16:69458460-69458469
30	ZNF143	chr16:69457966-69458745	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB7A	chr16:69458097-69458384	HepG2	liver:	n/a	n/a
32	MAFK	chr16:69458110-69458729	Hela-S3	cervix:	n/a	n/a
33	ZNF143	chr16:69458046-69458972	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr16:69458010-69459293	GM19099	blood:	n/a	n/a
35	TAF1	chr16:69457946-69458788	PFSK-1	brain:	n/a	n/a
36	HCFC1	chr16:69458106-69458929	K562	blood:	n/a	n/a
37	POLR2A	chr16:69458170-69458805	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr16:69458234-69458846	K562	blood:	n/a	n/a
39	MXI1	chr16:69458071-69459113	HepG2	liver:	n/a	n/a
40	POLR2A	chr16:69458043-69459171	GM15510	blood:	n/a	n/a
41	MAX	chr16:69457976-69459251	A549	lung:	n/a	n/a
42	NFYA	chr16:69458074-69458726	GM12878	blood:	n/a	chr16:69458461-69458471 chr16:69458298-69458313 chr16:69458333-69458346 chr16:69458301-69458311 chr16:69458299-69458313 chr16:69458298-69458313
43	CHD2	chr16:69458040-69458889	GM12878	blood:	n/a	chr16:69458797-69458807 chr16:69458379-69458389
44	SMC3	chr16:69458146-69459301	GM12878	blood:	n/a	n/a
45	NFYB	chr16:69457847-69458746	GM12878	blood:	n/a	chr16:69458461-69458471 chr16:69458298-69458313 chr16:69458333-69458346 chr16:69458301-69458311 chr16:69458299-69458313 chr16:69458418-69458433 chr16:69458298-69458313
46	SP4	chr16:69458325-69458779	H1-hESC	embryonic stem cell:	n/a	chr16:69458384-69458400 chr16:69458388-69458399
47	RUNX3	chr16:69457900-69458964	GM12878	blood:	n/a	n/a
48	NFYA	chr16:69458010-69458891	K562	blood:	n/a	chr16:69458461-69458471 chr16:69458298-69458313 chr16:69458333-69458346 chr16:69458301-69458311 chr16:69458299-69458313 chr16:69458298-69458313
49	YY1	chr16:69458294-69458907	GM12878	blood:	n/a	n/a
50	SETDB1	chr16:69458006-69458786	U2OS	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:69458329-69458379	GM12892	blood:	n/a
2	chr16:69458329-69458379	HUVEC	blood vessel:	n/a
3	chr16:69458329-69458379	GM12878	blood:	n/a
4	chr16:69458329-69458379	A549	lung:	n/a
5	chr16:69458329-69458379	NT2-D1	testis:	n/a
6	chr16:69458329-69458379	Caco-2	colon:	n/a
7	chr16:69458329-69458379	HEK293	kidney:	embryo
8	chr16:69458329-69458379	AG04449	skin:	fetal
9	chr16:69458329-69458379	HCF	heart:	n/a
10	chr16:69458329-69458379	NH-A	brain:	n/a
11	chr16:69458329-69458379	HRCEpiC	kidney:	n/a
12	chr16:69458329-69458379	NB4	blood:	n/a
13	chr16:69458329-69458379	AoSMC	blood vessel:	n/a
14	chr16:69458329-69458379	ECC-1	luminal epithelium:	n/a
15	chr16:69458329-69458379	PFSK-1	brain:	n/a
16	chr16:69458329-69458379	HNPCEpiC	eye:	n/a
17	chr16:69458329-69458379	HRE	kidney:	n/a
18	chr16:69458329-69458379	HL-60	blood:	n/a
19	chr16:69458329-69458379	SK-N-MC	brain:	n/a
20	chr16:69458329-69458379	Hepatocyte	liver:	n/a
21	chr16:69458329-69458379	HIPEpiC	eye:	n/a
22	chr16:69458329-69458379	LNCaP	prostate:	n/a
23	chr16:69458329-69458379	SK-N-SH_RA	brain:	n/a
24	chr16:69458329-69458379	Jurkat	blood:	n/a
25	chr16:69458329-69458379	BE2_C	brain:	n/a
26	chr16:69458329-69458379	PANC-1	pancreas:	n/a
27	chr16:69458329-69458379	GM12891	blood:	n/a
28	chr16:69458329-69458379	AG10803	skin:	n/a
29	chr16:69458329-69458379	NHDF-neo	bronchial:	n/a
30	chr16:69458329-69458379	H1-hESC	embryonic stem cell:	embryo
31	chr16:69458329-69458379	RPTEC	kidney:	n/a
32	chr16:69458329-69458379	CMK	blood:	n/a
33	chr16:69458329-69458379	PrEC	prostate:	n/a
34	chr16:69458329-69458379	AG09309	skin:	n/a
35	chr16:69458329-69458379	IMR90	lung:	fetal
36	chr16:69458329-69458379	T-47D	breast:	n/a
37	chr16:69458329-69458379	HCT-116	colon:	n/a
38	chr16:69458329-69458379	AG09319	gingival:	n/a
39	chr16:69458329-69458379	HepG2	liver:	n/a
40	chr16:69458329-69458379	GM06990	blood:	n/a
41	chr16:69458329-69458379	BJ	skin:	n/a
42	chr16:69458329-69458379	HPAEpiC	pulmonary alveolar:	n/a
43	chr16:69458329-69458379	K562	blood:	n/a
44	chr16:69458329-69458379	SK-N-SH	brain:	n/a
45	chr16:69458329-69458379	MCF10A-Er-Src	breast:	n/a
46	chr16:69458329-69458379	ovcar-3	ovarian:	n/a
47	chr16:69458329-69458379	HCPEpiC	choroid plexus:	n/a
48	chr16:69458329-69458379	HCM	heart:	n/a
49	chr16:69458329-69458379	HAEpiC	amniotic membrane:	n/a
50	chr16:69458329-69458379	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69457747..69460846-chr16:69598845..69601292,3	MCF-7	breast:
2	chr16:69457237..69459987-chr16:69598210..69601258,3	K562	blood:
3	chr11:62312821..62313690-chr16:69458253..69458783,2	Hela-S3	cervix:
4	chr16:69418455..69420510-chr16:69457015..69459227,2	MCF-7	breast:
5	chr16:69456628..69460851-chr16:69598482..69601931,4	MCF-7	breast:
6	chr1:147806517..147807246-chr16:69458323..69458854,2	Hela-S3	cervix:

Variant related genes	Relation type
CYB5B	TF binding region
CYB5B	CpG island
ENSG00000257058	Chromatin interaction
ENSG00000202408	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000132604	Chromatin interaction
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10048086	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs11075720	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs153058	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs246138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs246140	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246142	1.00[CEU][hapmap];0.95[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];0.98[ASN][1000 genomes]
rs246144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246145	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs246148	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4783708	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499227	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7185800	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7206737	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs728546	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs8064195	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs862349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1064808	chr16:69271190-69552951	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv542940	chr16:69271190-69552951	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs246143	LCAT	cis	parietal	SCAN
rs246143	ZNF23	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69452000-69458400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:69456800-69460000	Active TSS	GM12878-XiMat	blood
3	chr16:69457000-69458800	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr16:69457000-69459600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr16:69457200-69459000	Active TSS	Fetal Kidney	kidney
6	chr16:69457200-69459400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr16:69457200-69459600	Active TSS	Brain Anterior Caudate	brain
8	chr16:69457400-69458400	Flanking Active TSS	Dnd41	blood
9	chr16:69457400-69459000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr16:69457400-69459200	Active TSS	Osteobl	bone
11	chr16:69457400-69459400	Active TSS	NHEK	skin
12	chr16:69457400-69459600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:69457400-69459800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr16:69457400-69459800	Active TSS	NHDF-Ad	bronchial
15	chr16:69457600-69458600	Active TSS	Right Atrium	heart
16	chr16:69457600-69459000	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr16:69457600-69459000	Active TSS	Fetal Brain Female	brain
18	chr16:69457600-69459200	Active TSS	Pancreas	Pancrea
19	chr16:69457600-69459400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr16:69457600-69459600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr16:69457600-69459800	Active TSS	Brain Cingulate Gyrus	brain
22	chr16:69457600-69459800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:69457800-69458400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr16:69457800-69458400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr16:69457800-69458400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr16:69457800-69458400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr16:69457800-69458600	Active TSS	Rectal Smooth Muscle	rectum
28	chr16:69457800-69458800	Active TSS	Primary T cells from cord blood	blood
29	chr16:69457800-69458800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr16:69457800-69458800	Active TSS	Brain Germinal Matrix	brain
31	chr16:69457800-69459000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr16:69457800-69459000	Active TSS	Brain Substantia Nigra	brain
33	chr16:69457800-69459000	Active TSS	Fetal Lung	lung
34	chr16:69457800-69459000	Active TSS	Psoas Muscle	Psoas
35	chr16:69457800-69459000	Active TSS	K562	blood
36	chr16:69457800-69459200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr16:69457800-69459200	Active TSS	Left Ventricle	heart
38	chr16:69457800-69459200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr16:69457800-69459400	Active TSS	Brain Hippocampus Middle	brain
40	chr16:69457800-69459400	Active TSS	Colonic Mucosa	Colon
41	chr16:69457800-69459400	Active TSS	Colon Smooth Muscle	Colon
42	chr16:69457800-69459400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr16:69457800-69459400	Active TSS	Placenta	Placenta
44	chr16:69457800-69459400	Active TSS	Ovary	ovary
45	chr16:69457800-69459400	Active TSS	Right Ventricle	heart
46	chr16:69457800-69459400	Active TSS	Thymus	Thymus
47	chr16:69457800-69459600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:69457800-69459600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr16:69457800-69459600	Active TSS	Fetal Intestine Small	intestine
50	chr16:69457800-69459600	Active TSS	Stomach Smooth Muscle	stomach

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