Variant report

Variant	rs3761082
Chromosome Location	chr19:19249727-19249728
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	NFYB	chr19:19248922-19249782	GM12878	blood:	n/a	chr19:19249342-19249356 chr19:19249342-19249355 chr19:19249342-19249357 chr19:19249342-19249357 chr19:19249300-19249315 chr19:19249339-19249354 chr19:19249300-19249315
2	TCF7L2	chr19:19249094-19250138	HEK293	kidney:	n/a	chr19:19249443-19249452
3	SP1	chr19:19248754-19249827	HCT-116	colon:	n/a	chr19:19249301-19249322
4	ZMIZ1	chr19:19249052-19249786	K562	blood:	n/a	n/a
5	TCF7L2	chr19:19249022-19250116	HCT-116	colon:	n/a	chr19:19249443-19249452
6	KAP1	chr19:19249066-19250742	U2OS	brain:	n/a	n/a
7	TCF7L2	chr19:19249066-19249729	MCF-7	breast:	n/a	chr19:19249443-19249452
8	HCFC1	chr19:19249039-19249859	K562	blood:	n/a	n/a
9	GATA2	chr19:19249240-19249730	K562	blood:	n/a	n/a
10	MXI1	chr19:19248327-19249848	SK-N-SH	brain:	n/a	n/a
11	TCF7L2	chr19:19249036-19249941	PANC-1	pancreas:	n/a	chr19:19249443-19249452
12	HCFC1	chr19:19248492-19251341	Hela-S3	cervix:	n/a	n/a
13	CUX1	chr19:19249160-19249952	K562	blood:	n/a	chr19:19249437-19249446
14	RCOR1	chr19:19248766-19251323	IMR90	lung:	n/a	n/a
15	CREB1	chr19:19248552-19249799	HepG2	liver:	n/a	n/a
16	SMC3	chr19:19249555-19249784	HepG2	liver:	n/a	n/a
17	CBX3	chr19:19249335-19249895	K562	blood:	n/a	n/a
18	NFYA	chr19:19248932-19249763	K562	blood:	n/a	chr19:19249300-19249318 chr19:19249342-19249356 chr19:19249342-19249355 chr19:19249342-19249357 chr19:19249342-19249357 chr19:19249300-19249315 chr19:19249300-19249315
19	IRF1	chr19:19248674-19249755	K562	blood:	n/a	chr19:19249497-19249511 chr19:19249501-19249511
20	CBX3	chr19:19248864-19249822	K562	blood:	n/a	n/a
21	MAX	chr19:19248787-19249890	HCT-116	colon:	n/a	n/a
22	RCOR1	chr19:19248966-19249904	K562	blood:	n/a	n/a
23	TCF7L2	chr19:19249600-19250002	HepG2	liver:	n/a	n/a
24	TCF7L2	chr19:19248981-19249901	Hela-S3	cervix:	n/a	chr19:19249443-19249452
25	RCOR1	chr19:19249131-19250106	K562	blood:	n/a	n/a
26	RCOR1	chr19:19249057-19249737	HepG2	liver:	n/a	n/a
27	SP1	chr19:19248801-19249779	HCT-116	colon:	n/a	chr19:19249301-19249322
28	TCF7L2	chr19:19249193-19249776	Hela-S3	cervix:	n/a	chr19:19249443-19249452
29	ZC3H11A	chr19:19249057-19249738	K562	blood:	n/a	n/a
30	MAX	chr19:19248538-19249847	HepG2	liver:	n/a	n/a
31	GATA2	chr19:19249011-19249783	SH-SY5Y	brain:	n/a	n/a
32	BHLHE40	chr19:19248895-19249728	K562	blood:	n/a	n/a
33	GATA3	chr19:19249304-19250099	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19110446..19112706-chr19:19249523..19251357,2	K562	blood:
2	chr19:19172595..19175925-chr19:19247411..19251399,4	MCF-7	breast:
3	chr19:19249614..19251216-chr19:19284548..19287281,2	K562	blood:
4	chr19:19163080..19165123-chr19:19247773..19249964,2	MCF-7	breast:
5	chr19:19229446..19234006-chr19:19241302..19251526,15	K562	blood:
6	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
7	chr19:19164507..19166528-chr19:19249184..19251105,2	K562	blood:
8	chr19:19239875..19242628-chr19:19248589..19251207,2	MCF-7	breast:
9	chr19:19231565..19233843-chr19:19248127..19250421,2	MCF-7	breast:

Variant related genes	Relation type
TMEM161A	TF binding region
ENSG00000181035	Chromatin interaction
ENSG00000064545	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10417318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787041	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4353576	0.82[JPT][hapmap]
rs4808925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248977	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7250310	0.82[JPT][hapmap]
rs72993464	0.83[ASN][1000 genomes]
rs72993466	0.91[ASN][1000 genomes]
rs72993474	0.91[ASN][1000 genomes]
rs72993480	0.87[ASN][1000 genomes]
rs72993489	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761082	COMP	cis	brain	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19247800-19249800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19247800-19249800	Flanking Active TSS	Dnd41	blood
3	chr19:19248200-19249800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:19248400-19249800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:19248400-19249800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:19248600-19249800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr19:19248600-19249800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:19248600-19249800	Active TSS	Brain Anterior Caudate	brain
9	chr19:19248800-19249800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:19248800-19249800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr19:19248800-19249800	Active TSS	Brain Angular Gyrus	brain
12	chr19:19248800-19249800	Active TSS	Brain Germinal Matrix	brain
13	chr19:19248800-19249800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:19248800-19249800	Active TSS	Duodenum Mucosa	Duodenum
15	chr19:19248800-19249800	Active TSS	Ovary	ovary
16	chr19:19248800-19249800	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:19249000-19249800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr19:19249000-19249800	Active TSS	Thymus	Thymus
19	chr19:19249200-19249800	Active TSS	Primary hematopoietic stem cells	blood
20	chr19:19249200-19249800	Active TSS	Stomach Smooth Muscle	stomach
21	chr19:19249200-19250000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr19:19249200-19256600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:19249400-19249800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr19:19249400-19249800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr19:19249400-19249800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:19249400-19249800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr19:19249400-19249800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:19249400-19249800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr19:19249400-19249800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr19:19249400-19249800	Enhancers	Spleen	Spleen
31	chr19:19249400-19249800	Enhancers	GM12878-XiMat	blood
32	chr19:19249400-19249800	Flanking Active TSS	Hela-S3	cervix
33	chr19:19249400-19250000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr19:19249400-19250600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr19:19249400-19250600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:19249400-19250600	Weak transcription	Placenta	Placenta
37	chr19:19249400-19250600	Enhancers	Fetal Thymus	thymus
38	chr19:19249400-19250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:19249400-19250800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:19249400-19250800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:19249400-19250800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:19249400-19256600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:19249400-19256800	Weak transcription	Lung	lung
44	chr19:19249400-19257400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:19249400-19259600	Weak transcription	Aorta	Aorta
46	chr19:19249400-19259800	Weak transcription	Left Ventricle	heart
47	chr19:19249400-19271200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:19249600-19249800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr19:19249600-19249800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:19249600-19249800	Active TSS	Adipose Nuclei	Adipose

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