Variant report

Variant	rs6799550
Chromosome Location	chr3:98242103-98242104
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	ETS1	chr3:98241300-98242177	GM12878	blood:	n/a	chr3:98241866-98241873 chr3:98241942-98241955 chr3:98241941-98241954
2	FOXM1	chr3:98240683-98242377	GM12878	blood:	n/a	n/a
3	YY1	chr3:98240935-98242161	GM12892	blood:	n/a	chr3:98241920-98241934
4	BCLAF1	chr3:98240446-98243136	GM12878	blood:	n/a	n/a
5	NFATC1	chr3:98240387-98245434	GM12878	blood:	n/a	n/a
6	MAX	chr3:98241255-98242227	A549	lung:	n/a	n/a
7	REST	chr3:98240553-98242239	H1-neurons	neurons:	n/a	chr3:98241953-98241973
8	TAF1	chr3:98240950-98242117	GM12878	blood:	n/a	n/a
9	GATA2	chr3:98240707-98242143	SH-SY5Y	brain:	n/a	chr3:98241292-98241301 chr3:98241294-98241301 chr3:98241287-98241308 chr3:98241294-98241301 chr3:98241294-98241301 chr3:98241292-98241302
10	USF2	chr3:98241544-98242120	GM12878	blood:	n/a	n/a
11	YY1	chr3:98241533-98242117	SK-N-SH_RA	brain:	n/a	chr3:98241920-98241934
12	PAX5	chr3:98241407-98242217	GM12878	blood:	n/a	n/a
13	SP1	chr3:98240925-98242398	HCT-116	colon:	n/a	chr3:98241813-98241824 chr3:98241871-98241882
14	SIN3AK20	chr3:98240800-98242249	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:98240930-98242134	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:98241337-98242115	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr3:98239736-98242420	GM12878	blood:	n/a	n/a
18	TAF1	chr3:98240954-98242133	ECC-1	luminal epithelium:	n/a	n/a
19	HCFC1	chr3:98240666-98242447	Hela-S3	cervix:	n/a	n/a
20	TEAD4	chr3:98241531-98242173	ECC-1	luminal epithelium:	n/a	n/a
21	EP300	chr3:98240968-98242233	K562	blood:	n/a	chr3:98241917-98241933
22	JUND	chr3:98241073-98242245	H1-hESC	embryonic stem cell:	n/a	chr3:98241281-98241291 chr3:98241152-98241160 chr3:98241152-98241159 chr3:98241282-98241290
23	CBX3	chr3:98241538-98242131	K562	blood:	n/a	n/a
24	STAT5A	chr3:98240435-98242976	GM12878	blood:	n/a	n/a
25	TBP	chr3:98241749-98242142	Hela-S3	cervix:	n/a	n/a
26	BCL3	chr3:98240855-98242262	GM12878	blood:	n/a	n/a
27	POU2F2	chr3:98240907-98242235	GM12878	blood:	n/a	chr3:98241339-98241360
28	YY1	chr3:98241540-98242169	ECC-1	luminal epithelium:	n/a	chr3:98241920-98241934
29	IRF1	chr3:98241605-98242119	K562	blood:	n/a	n/a
30	POLR2A	chr3:98241009-98242135	NB4	blood:	n/a	n/a
31	POLR2A	chr3:98241419-98242125	HL-60	blood:	n/a	n/a
32	POLR2A	chr3:98240581-98242251	PBDE	blood:	n/a	n/a
33	NRF1	chr3:98241680-98242104	GM12878	blood:	n/a	chr3:98241922-98241931 chr3:98241926-98241935
34	GABPA	chr3:98241449-98242194	A549	lung:	n/a	chr3:98241922-98241931 chr3:98241926-98241935
35	ZMIZ1	chr3:98241236-98242127	K562	blood:	n/a	n/a
36	MXI1	chr3:98240962-98242125	HepG2	liver:	n/a	n/a
37	CREB1	chr3:98241240-98242198	HepG2	liver:	n/a	n/a
38	SIX5	chr3:98241667-98242105	GM12878	blood:	n/a	chr3:98241865-98241874 chr3:98241944-98241953 chr3:98241941-98241955 chr3:98241942-98241951
39	POLR2A	chr3:98240046-98245016	GM12892	blood:	n/a	n/a
40	ZNF143	chr3:98241041-98242303	Hela-S3	cervix:	n/a	chr3:98241935-98241953 chr3:98242212-98242231 chr3:98241942-98241951 chr3:98241858-98241876 chr3:98241865-98241874 chr3:98241931-98241946 chr3:98241944-98241953
41	ELF1	chr3:98241524-98242247	MCF-7	breast:	n/a	n/a
42	MAX	chr3:98240933-98242152	SK-N-SH	brain:	n/a	n/a
43	NFIC	chr3:98240869-98242198	ECC-1	luminal epithelium:	n/a	n/a
44	BRCA1	chr3:98241567-98242117	GM12878	blood:	n/a	n/a
45	ZNF143	chr3:98240933-98242275	K562	blood:	n/a	chr3:98241935-98241953 chr3:98242212-98242231 chr3:98241942-98241951 chr3:98241858-98241876 chr3:98241865-98241874 chr3:98241931-98241946 chr3:98241944-98241953
46	HA-E2F1	chr3:98240870-98242261	MCF-7	breast:	n/a	chr3:98241917-98241927
47	POLR2A	chr3:98240411-98244872	GM12891	blood:	n/a	n/a
48	CREB1	chr3:98241342-98242229	HepG2	liver:	n/a	n/a
49	GABPA	chr3:98241430-98242282	SK-N-SH	brain:	n/a	chr3:98241922-98241931 chr3:98241926-98241935
50	POU2F2	chr3:98240921-98242368	GM12891	blood:	n/a	chr3:98241339-98241360

No.	Distal block	Cell Line	Cell type
1	chr3:98240168..98242320-chr3:98310651..98312763,2	K562	blood:
2	chr3:98241176..98243261-chr3:98243368..98246193,2	MCF-7	breast:
3	chr3:98234756..98237883-chr3:98238523..98242398,6	K562	blood:
4	chr3:98241309..98243234-chr3:98301701..98304609,2	K562	blood:

Variant related genes	Relation type
CLDND1	TF binding region
ENSG00000080819	Chromatin interaction
ENSG00000250562	Chromatin interaction
ENSG00000080822	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1461155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1529046	0.82[YRI][hapmap]
rs16839845	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230344	1.00[YRI][hapmap]
rs2306065	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807441	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811242	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819403	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834252	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834774	chr3:98108423-98274064	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6799550	VWDE	trans	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98240000-98242200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:98240000-98242200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:98240000-98242200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr3:98240000-98242400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:98240000-98242400	Active TSS	Fetal Brain Male	brain
6	chr3:98240200-98242200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:98240200-98242200	Active TSS	Psoas Muscle	Psoas
8	chr3:98240200-98242400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:98240200-98242400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:98240200-98242400	Active TSS	Stomach Smooth Muscle	stomach
11	chr3:98240400-98242200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:98240400-98242200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:98240400-98242200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:98240400-98242200	Active TSS	Brain Substantia Nigra	brain
15	chr3:98240400-98242200	Active TSS	Colonic Mucosa	Colon
16	chr3:98240400-98242200	Active TSS	Fetal Brain Female	brain
17	chr3:98240400-98242400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:98240400-98242400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:98240400-98242400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:98240600-98242200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr3:98240600-98242200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:98240600-98242200	Active TSS	Fetal Muscle Trunk	muscle
23	chr3:98240600-98242200	Active TSS	Left Ventricle	heart
24	chr3:98240600-98242200	Active TSS	Ovary	ovary
25	chr3:98240600-98242200	Active TSS	Right Ventricle	heart
26	chr3:98240600-98242400	Active TSS	Brain Hippocampus Middle	brain
27	chr3:98240600-98242400	Active TSS	NH-A	brain
28	chr3:98240800-98242200	Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:98240800-98242200	Active TSS	Aorta	Aorta
30	chr3:98240800-98242200	Active TSS	Brain Angular Gyrus	brain
31	chr3:98240800-98242200	Active TSS	Brain Cingulate Gyrus	brain
32	chr3:98240800-98242200	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:98240800-98242200	Active TSS	Fetal Kidney	kidney
34	chr3:98240800-98242200	Active TSS	Placenta Amnion	Placenta Amnion
35	chr3:98240800-98242400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:98240800-98242400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:98240800-98242400	Bivalent/Poised TSS	HepG2	liver
38	chr3:98240800-98242600	Active TSS	Colon Smooth Muscle	Colon
39	chr3:98241000-98242200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:98241000-98242200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:98241000-98242200	Active TSS	Fetal Lung	lung
42	chr3:98241000-98242200	Active TSS	Osteobl	bone
43	chr3:98241000-98242400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:98241000-98242400	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr3:98241000-98242800	Active TSS	Thymus	Thymus
46	chr3:98241200-98242400	Active TSS	Adipose Nuclei	Adipose
47	chr3:98241800-98242200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:98241800-98242200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:98241800-98242200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:98241800-98242200	Enhancers	Placenta	Placenta

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