Variant report

Variant	rs35028754
Chromosome Location	chr16:71879672-71879673
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	SRF	chr16:71879423-71880275	MCF-7	breast:	n/a	chr16:71879697-71879707 chr16:71879693-71879703
2	RELA	chr16:71879440-71880040	GM19193	blood:	n/a	n/a
3	TCF12	chr16:71879466-71880328	ECC-1	luminal epithelium:	n/a	chr16:71880142-71880149
4	MAX	chr16:71879430-71880076	A549	lung:	n/a	n/a
5	IRF4	chr16:71879626-71879997	GM12878	blood:	n/a	n/a
6	CTCF	chr16:71879640-71879790	AoAF	blood vessel:	n/a	chr16:71879748-71879766 chr16:71879751-71879760
7	TAF1	chr16:71879604-71880086	SK-N-SH	brain:	n/a	n/a
8	CCNT2	chr16:71879624-71880181	K562	blood:	n/a	chr16:71879926-71879935
9	CEBPB	chr16:71879626-71880041	Hela-S3	cervix:	n/a	chr16:71879834-71879845
10	PAX5	chr16:71879488-71880141	GM12892	blood:	n/a	chr16:71880066-71880075
11	SP1	chr16:71879422-71880141	HCT-116	colon:	n/a	chr16:71879857-71879866 chr16:71879611-71879621 chr16:71879855-71879867 chr16:71879855-71879867 chr16:71879692-71879704 chr16:71879692-71879704 chr16:71879856-71879865 chr16:71879611-71879620
12	FOXA1	chr16:71879499-71880036	HepG2	liver:	n/a	n/a
13	EP300	chr16:71879653-71880047	HepG2	liver:	n/a	chr16:71879940-71879949
14	BRCA1	chr16:71879658-71880084	HepG2	liver:	n/a	n/a
15	IRF1	chr16:71879589-71880057	K562	blood:	n/a	chr16:71879855-71879869
16	POLR2A	chr16:71879508-71880335	H1-neurons	neurons:	n/a	n/a
17	SRF	chr16:71879666-71880069	H1-hESC	embryonic stem cell:	n/a	chr16:71879697-71879707 chr16:71879693-71879703
18	POLR2A	chr16:71879555-71880108	HepG2	liver:	n/a	n/a
19	EBF1	chr16:71879508-71879975	GM12878	blood:	n/a	n/a
20	CHD2	chr16:71879548-71880154	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr16:71879481-71880107	HL-60	blood:	n/a	n/a
22	ZKSCAN1	chr16:71879610-71880026	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr16:71879586-71880077	HepG2	liver:	n/a	n/a
24	ELF1	chr16:71879375-71880741	GM12878	blood:	n/a	chr16:71879939-71879951 chr16:71880266-71880279
25	MYC	chr16:71879657-71879983	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr16:71879560-71879710	HRE	kidney:	n/a	n/a
27	POLR2A	chr16:71879344-71880799	K562	blood:	n/a	n/a
28	BCL3	chr16:71879509-71880092	A549	lung:	n/a	chr16:71879938-71879951
29	POLR2A	chr16:71879514-71880132	K562	blood:	n/a	n/a
30	MTA3	chr16:71879329-71879929	GM12878	blood:	n/a	n/a
31	POLR2A	chr16:71879425-71880089	U87	brain:	n/a	n/a
32	CEBPB	chr16:71879622-71880024	A549	lung:	n/a	chr16:71879834-71879845
33	ATF3	chr16:71879558-71880084	GM12878	blood:	n/a	chr16:71879702-71879722 chr16:71879713-71879722 chr16:71879835-71879855 chr16:71879832-71879845 chr16:71879871-71879891 chr16:71879834-71879845 chr16:71879834-71879845
34	GTF2F1	chr16:71879653-71880046	H1-hESC	embryonic stem cell:	n/a	n/a
35	TCF12	chr16:71879566-71880014	A549	lung:	n/a	n/a
36	POLR2A	chr16:71879553-71880193	HUVEC	blood vessel:	n/a	n/a
37	NFIC	chr16:71878934-71880136	GM12878	blood:	n/a	n/a
38	MXI1	chr16:71879519-71880141	GM12878	blood:	n/a	chr16:71879714-71879723
39	MTA3	chr16:71879302-71880914	GM12878	blood:	n/a	n/a
40	ZNF143	chr16:71879451-71880023	GM12878	blood:	n/a	chr16:71879973-71879992 chr16:71879974-71879989 chr16:71879900-71879910
41	GABPA	chr16:71879633-71880063	HepG2	liver:	n/a	n/a
42	POLR2A	chr16:71879387-71880692	Hela-S3	cervix:	n/a	n/a
43	YY1	chr16:71879411-71880290	GM12878	blood:	n/a	chr16:71879944-71879958 chr16:71879938-71879947
44	TAF1	chr16:71879572-71880059	PFSK-1	brain:	n/a	n/a
45	TAF1	chr16:71879543-71880320	HepG2	liver:	n/a	n/a
46	RFX5	chr16:71879628-71880032	HepG2	liver:	n/a	n/a
47	ARID3A	chr16:71879635-71879838	K562	blood:	n/a	n/a
48	GABPA	chr16:71879445-71880249	MCF-7	breast:	n/a	chr16:71880099-71880108
49	USF2	chr16:71879560-71879979	H1-hESC	embryonic stem cell:	n/a	chr16:71879712-71879723 chr16:71879713-71879722 chr16:71879714-71879723 chr16:71879707-71879728
50	ATF3	chr16:71879533-71880070	HepG2	liver:	n/a	chr16:71879702-71879722 chr16:71879713-71879722 chr16:71879835-71879855 chr16:71879832-71879845 chr16:71879871-71879891 chr16:71879834-71879845 chr16:71879834-71879845

No.	Distal block	Cell Line	Cell type
1	chr16:71879516..71883331-chr16:71913609..71918904,8	MCF-7	breast:
2	chr16:71841032..71844957-chr16:71878188..71881982,18	MCF-7	breast:
3	chr16:71878397..71880298-chr16:71917810..71919339,2	MCF-7	breast:
4	chr16:71879435..71880022-chr2:208030843..208031579,2	MCF-7	breast:
5	chr16:71840441..71845295-chr16:71875076..71881716,14	K562	blood:
6	chr16:71756009..71758513-chr16:71878989..71881221,2	K562	blood:
7	chr16:71878736..71881297-chr20:57268088..57270906,2	MCF-7	breast:
8	chr16:71878320..71880402-chr16:71929242..71933378,4	MCF-7	breast:
9	chr16:71878006..71880307-chr16:74330687..74332965,2	MCF-7	breast:
10	chr16:71842768..71843766-chr16:71879326..71880235,4	MCF-7	breast:
11	chr16:71841284..71844520-chr16:71878157..71881366,4	K562	blood:
12	chr16:71879510..71881419-chr16:72127750..72129828,2	MCF-7	breast:
13	chr16:71874199..71877038-chr16:71877989..71879854,2	MCF-7	breast:
14	chr16:71879026..71881212-chr16:71914841..71917763,3	MCF-7	breast:
15	chr16:71832833..71836832-chr16:71876405..71879704,4	K562	blood:
16	chr16:71878378..71882676-chr16:71918678..71922110,3	K562	blood:
17	chr16:71755537..71758357-chr16:71878950..71881033,2	K562	blood:
18	chr16:71841846..71843774-chr16:71878337..71881293,3	MCF-7	breast:

Variant related genes	Relation type
ATXN1L	TF binding region
IST1	TF binding region
ENSG00000140830	Chromatin interaction
ENSG00000215440	Chromatin interaction
ENSG00000103035	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000040199	Chromatin interaction
ENSG00000140829	Chromatin interaction
ENSG00000118263	Chromatin interaction
ENSG00000261513	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000261765	Chromatin interaction
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10500567	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10852507	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11075906	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11639843	0.82[ASN][1000 genomes]
rs11640135	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644740	0.82[ASN][1000 genomes]
rs11865456	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12149307	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12149325	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12149917	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445564	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12445641	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12448086	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12921279	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12921459	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12927691	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12934512	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13330178	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17357420	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17358402	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28667298	0.89[ASN][1000 genomes]
rs2878494	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3088285	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34029919	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34101687	0.82[ASN][1000 genomes]
rs34664834	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35209006	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35404791	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35535529	0.96[EUR][1000 genomes]
rs35595148	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36182990	0.82[ASN][1000 genomes]
rs3751820	0.91[EUR][1000 genomes]
rs4528577	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71384781	0.92[EUR][1000 genomes]
rs71384782	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71386939	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71386940	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71386942	0.82[ASN][1000 genomes]
rs7185027	0.88[EUR][1000 genomes]
rs7188591	0.92[EUR][1000 genomes]
rs7191848	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7195988	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7197486	0.92[EUR][1000 genomes]
rs7198834	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7200447	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73586164	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8046044	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8049508	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8050058	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8052358	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8053906	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8063657	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9940234	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71878800-71880400	Active TSS	Colon Smooth Muscle	Colon
2	chr16:71879000-71880000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr16:71879000-71880200	Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr16:71879000-71880200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr16:71879000-71880400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:71879000-71880400	Active TSS	Adipose Nuclei	Adipose
7	chr16:71879000-71880400	Active TSS	Colonic Mucosa	Colon
8	chr16:71879000-71880400	Active TSS	Duodenum Mucosa	Duodenum
9	chr16:71879000-71880400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr16:71879000-71880400	Active TSS	Rectal Smooth Muscle	rectum
11	chr16:71879000-71880600	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr16:71879000-71880600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:71879000-71880600	Active TSS	Brain Substantia Nigra	brain
14	chr16:71879000-71880800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr16:71879000-71880800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr16:71879000-71880800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr16:71879000-71880800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr16:71879000-71880800	Active TSS	Aorta	Aorta
19	chr16:71879000-71880800	Active TSS	A549	lung
20	chr16:71879000-71880800	Active TSS	HSMM	muscle
21	chr16:71879000-71880800	Active TSS	NHDF-Ad	bronchial
22	chr16:71879000-71881000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr16:71879000-71881000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr16:71879000-71881000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:71879000-71881000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:71879000-71881000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr16:71879000-71881000	Active TSS	Fetal Kidney	kidney
28	chr16:71879000-71881400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr16:71879000-71881400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr16:71879200-71879800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:71879200-71879800	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr16:71879200-71879800	Active TSS	Brain Germinal Matrix	brain
33	chr16:71879200-71879800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr16:71879200-71880000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr16:71879200-71880200	Active TSS	Primary T cells from cord blood	blood
36	chr16:71879200-71880200	Active TSS	Liver	Liver
37	chr16:71879200-71880200	Active TSS	Placenta	Placenta
38	chr16:71879200-71880200	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr16:71879200-71880600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:71879200-71880600	Active TSS	Brain Anterior Caudate	brain
41	chr16:71879200-71880600	Active TSS	Brain Hippocampus Middle	brain
42	chr16:71879200-71880600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr16:71879200-71880600	Active TSS	Fetal Brain Female	brain
44	chr16:71879200-71880600	Active TSS	Fetal Lung	lung
45	chr16:71879200-71880600	Active TSS	Fetal Stomach	stomach
46	chr16:71879200-71880600	Active TSS	Left Ventricle	heart
47	chr16:71879200-71880600	Active TSS	Pancreas	Pancrea
48	chr16:71879200-71880600	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr16:71879200-71880600	Active TSS	Thymus	Thymus
50	chr16:71879200-71880600	Active TSS	K562	blood

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