Variant report

Variant	rs3809633
Chromosome Location	chr16:81347747-81347748
allele	C/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	GATA3	chr16:81347322-81347811	SH-SY5Y	brain:	n/a	n/a
2	MYBL2	chr16:81347296-81348886	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:81347117-81348145	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr16:81347635-81348892	PBDE	blood:	n/a	n/a
5	SIN3A	chr16:81347094-81349480	H1-hESC	embryonic stem cell:	n/a	chr16:81349182-81349195 chr16:81349360-81349373
6	POLR2A	chr16:81347074-81348885	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBP	chr16:81347136-81347747	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr16:81347419-81348754	H1-neurons	neurons:	n/a	chr16:81348122-81348130
9	EGR1	chr16:81347460-81348959	HCT-116	colon:	n/a	chr16:81348498-81348511 chr16:81347790-81347800 chr16:81347790-81347800 chr16:81348500-81348510 chr16:81348498-81348511 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81348501-81348510 chr16:81348497-81348512 chr16:81347789-81347802 chr16:81348500-81348510 chr16:81347786-81347800 chr16:81348470-81348484 chr16:81348498-81348511 chr16:81348498-81348512 chr16:81348498-81348511 chr16:81347789-81347799 chr16:81348494-81348516 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81348499-81348510 chr16:81347790-81347799 chr16:81347539-81347563 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
10	SIN3AK20	chr16:81347289-81349895	MCF-7	breast:	n/a	n/a
11	CHD2	chr16:81347397-81347849	HepG2	liver:	n/a	n/a
12	MXI1	chr16:81346949-81350033	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr16:81346947-81349653	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF7L2	chr16:81347400-81347925	Hela-S3	cervix:	n/a	chr16:81347602-81347612 chr16:81347599-81347613 chr16:81347602-81347611
15	YY1	chr16:81347213-81348048	H1-hESC	embryonic stem cell:	n/a	chr16:81347788-81347797
16	RUNX3	chr16:81347747-81348888	GM12878	blood:	n/a	n/a
17	CHD1	chr16:81347036-81348799	H1-hESC	embryonic stem cell:	n/a	chr16:81348543-81348550
18	EGR1	chr16:81347449-81348956	HCT-116	colon:	n/a	chr16:81348498-81348511 chr16:81347790-81347800 chr16:81347790-81347800 chr16:81348500-81348510 chr16:81348498-81348511 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81348501-81348510 chr16:81348497-81348512 chr16:81347789-81347802 chr16:81348500-81348510 chr16:81347786-81347800 chr16:81348470-81348484 chr16:81348498-81348511 chr16:81348498-81348512 chr16:81348498-81348511 chr16:81347789-81347799 chr16:81348494-81348516 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81348499-81348510 chr16:81347790-81347799 chr16:81347539-81347563 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
19	RCOR1	chr16:81347380-81350098	IMR90	lung:	n/a	n/a
20	RCOR1	chr16:81347403-81347866	HepG2	liver:	n/a	n/a
21	GATA2	chr16:81347402-81347797	SH-SY5Y	brain:	n/a	n/a
22	EGR1	chr16:81347567-81347980	K562	blood:	n/a	chr16:81347790-81347800 chr16:81347790-81347800 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81347789-81347802 chr16:81347786-81347800 chr16:81347789-81347799 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81347790-81347799 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
23	EGR1	chr16:81347379-81348775	MCF-7	breast:	n/a	chr16:81348498-81348511 chr16:81347790-81347800 chr16:81347790-81347800 chr16:81348500-81348510 chr16:81348498-81348511 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81348501-81348510 chr16:81348497-81348512 chr16:81347789-81347802 chr16:81348500-81348510 chr16:81347786-81347800 chr16:81348470-81348484 chr16:81348498-81348511 chr16:81348498-81348512 chr16:81348498-81348511 chr16:81347789-81347799 chr16:81348494-81348516 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81348499-81348510 chr16:81347790-81347799 chr16:81347539-81347563 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
24	POLR2A	chr16:81347398-81349016	H1-neurons	neurons:	n/a	n/a
25	EGR1	chr16:81347561-81348134	K562	blood:	n/a	chr16:81347790-81347800 chr16:81347790-81347800 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81347789-81347802 chr16:81347786-81347800 chr16:81347789-81347799 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81347790-81347799 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
26	POLR2A	chr16:81347088-81348915	H1-hESC	embryonic stem cell:	n/a	n/a
27	TEAD4	chr16:81347015-81347772	H1-hESC	embryonic stem cell:	n/a	chr16:81347498-81347507
28	TAF1	chr16:81347042-81348902	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr16:81347444-81348969	H1-neurons	neurons:	n/a	n/a
30	MAX	chr16:81347219-81347790	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr16:81347254-81347768	H1-hESC	embryonic stem cell:	n/a	n/a
32	GATA3	chr16:81347324-81347874	MCF-7	breast:	n/a	n/a
33	REST	chr16:81347127-81349140	H1-neurons	neurons:	n/a	chr16:81348978-81348991 chr16:81348122-81348130
34	TCF12	chr16:81347544-81348829	A549	lung:	n/a	chr16:81347566-81347573
35	EGR1	chr16:81347571-81347932	H1-hESC	embryonic stem cell:	n/a	chr16:81347790-81347800 chr16:81347790-81347800 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81347789-81347802 chr16:81347786-81347800 chr16:81347789-81347799 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81347790-81347799 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
36	TEAD4	chr16:81347068-81347800	HepG2	liver:	n/a	chr16:81347498-81347507
37	EGR1	chr16:81347712-81347941	GM12878	blood:	n/a	chr16:81347790-81347800 chr16:81347790-81347800 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81347789-81347802 chr16:81347786-81347800 chr16:81347789-81347799 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81347790-81347799 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
38	ESRRA	chr16:81347218-81348857	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81109518..81111024-chr16:81347327..81349963,2	K562	blood:
2	chr16:81038258..81040784-chr16:81347032..81349945,2	K562	blood:
3	chr16:81347539..81350872-chr16:81478035..81482618,4	MCF-7	breast:
4	chr16:81038653..81041025-chr16:81346635..81349129,2	MCF-7	breast:
5	chr16:81110316..81112473-chr16:81346981..81348533,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCSH-1	chr16:81345111-81348378	NONHSAT143942

Variant related genes	Relation type
ENSG00000260495	TF binding region
GAN	TF binding region
ENSG00000166455	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000153815	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10454708	0.84[EUR][1000 genomes]
rs12149852	0.84[EUR][1000 genomes]
rs12924233	0.96[EUR][1000 genomes]
rs3809632	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4468614	0.88[EUR][1000 genomes]
rs4522413	0.84[EUR][1000 genomes]
rs4598907	0.84[EUR][1000 genomes]
rs4888135	0.92[EUR][1000 genomes]
rs4888137	0.84[EUR][1000 genomes]
rs4888143	0.85[ASN][1000 genomes]
rs6564868	0.84[EUR][1000 genomes]
rs7184259	0.84[EUR][1000 genomes]
rs7195134	0.88[EUR][1000 genomes]
rs7196075	0.84[EUR][1000 genomes]
rs8060840	0.84[EUR][1000 genomes]
rs9940292	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
5	nsv522890	chr16:81341363-81348396	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr16:81346600-81349400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr16:81346800-81348600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:81346800-81349400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr16:81346800-81349400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr16:81346800-81349800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr16:81346800-81350200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr16:81347000-81347800	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr16:81347000-81347800	Flanking Active TSS	Fetal Brain Male	brain
9	chr16:81347000-81347800	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr16:81347000-81347800	Enhancers	Small Intestine	intestine
11	chr16:81347000-81347800	Enhancers	Spleen	Spleen
12	chr16:81347000-81347800	Flanking Active TSS	GM12878-XiMat	blood
13	chr16:81347000-81348000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr16:81347000-81348000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr16:81347000-81348000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr16:81347000-81348000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:81347000-81348000	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr16:81347000-81348000	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr16:81347000-81348000	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr16:81347000-81348000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr16:81347000-81348000	Flanking Active TSS	Fetal Brain Female	brain
22	chr16:81347000-81348000	Flanking Active TSS	Dnd41	blood
23	chr16:81347000-81348000	Flanking Active TSS	Hela-S3	cervix
24	chr16:81347000-81348000	Flanking Active TSS	NH-A	brain
25	chr16:81347000-81348200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr16:81347000-81349400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr16:81347000-81349600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr16:81347000-81349600	Active TSS	NHLF	lung
29	chr16:81347000-81349800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr16:81347000-81350000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr16:81347000-81350000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr16:81347000-81350200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:81347200-81347800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:81347200-81347800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr16:81347200-81347800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr16:81347200-81347800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr16:81347200-81347800	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr16:81347200-81347800	Flanking Active TSS	Gastric	stomach
39	chr16:81347200-81347800	Enhancers	Pancreas	Pancrea
40	chr16:81347200-81347800	Flanking Active TSS	NHDF-Ad	bronchial
41	chr16:81347200-81348000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr16:81347200-81348000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr16:81347200-81348000	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr16:81347200-81348000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr16:81347200-81348000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr16:81347200-81348000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr16:81347200-81348000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr16:81347200-81348000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr16:81347200-81348000	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr16:81347200-81348000	Flanking Active TSS	Colon Smooth Muscle	Colon

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