Variant report

Variant	rs2279699
Chromosome Location	chr19:41284398-41284399
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	TEAD4	chr19:41282840-41284622	K562	blood:	n/a	n/a
2	NR2F2	chr19:41283041-41285265	K562	blood:	n/a	n/a
3	HEY1	chr19:41284110-41284400	HepG2	liver:	n/a	chr19:41284233-41284248 chr19:41284130-41284145 chr19:41284232-41284247
4	POLR2A	chr19:41282824-41285023	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:41283024-41284454	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:41283667-41284589	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:41283077-41284413	GM10847	blood:	n/a	n/a
8	POLR2A	chr19:41283144-41284860	K562	blood:	n/a	n/a
9	NFYB	chr19:41283168-41284690	Hela-S3	cervix:	n/a	chr19:41283980-41283992 chr19:41283981-41283996
10	HEY1	chr19:41283131-41284814	HepG2	liver:	n/a	chr19:41284233-41284248 chr19:41284130-41284145 chr19:41284232-41284247
11	POLR2A	chr19:41283262-41284653	PANC-1	pancreas:	n/a	n/a
12	PBX3	chr19:41283560-41284991	A549	lung:	n/a	chr19:41283827-41283836 chr19:41283651-41283660
13	YY1	chr19:41283524-41284990	A549	lung:	n/a	chr19:41284243-41284265 chr19:41284226-41284240 chr19:41284241-41284258 chr19:41284237-41284246 chr19:41284242-41284254 chr19:41284382-41284391 chr19:41284235-41284246 chr19:41284143-41284152
14	MAZ	chr19:41283091-41284792	K562	blood:	n/a	n/a
15	SP1	chr19:41283683-41284666	K562	blood:	n/a	chr19:41284001-41284013 chr19:41284602-41284611 chr19:41284139-41284151 chr19:41284383-41284392 chr19:41284360-41284369 chr19:41284381-41284393 chr19:41284378-41284392 chr19:41284052-41284064 chr19:41284359-41284371 chr19:41284002-41284016 chr19:41284382-41284392 chr19:41284601-41284611 chr19:41284002-41284012 chr19:41284383-41284392 chr19:41283866-41283875 chr19:41284003-41284012 chr19:41284053-41284062 chr19:41284356-41284370 chr19:41284007-41284014 chr19:41284002-41284011 chr19:41284382-41284391 chr19:41284600-41284612 chr19:41284600-41284612 chr19:41284052-41284064 chr19:41284602-41284611 chr19:41284361-41284370 chr19:41284002-41284012 chr19:41284053-41284067 chr19:41284001-41284012 chr19:41284601-41284611 chr19:41284181-41284195 chr19:41284001-41284013 chr19:41284136-41284150 chr19:41284360-41284370 chr19:41284140-41284149 chr19:41284359-41284371 chr19:41284381-41284393 chr19:41284139-41284151 chr19:41284597-41284611 chr19:41284382-41284392 chr19:41284002-41284011 chr19:41284054-41284063 chr19:41284601-41284610
16	POLR2A	chr19:41282793-41284992	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3AK20	chr19:41284028-41284417	K562	blood:	n/a	n/a
18	RUNX3	chr19:41282646-41285107	GM12878	blood:	n/a	n/a
19	STAT1	chr19:41283046-41284778	GM12878	blood:	n/a	chr19:41283681-41283704
20	RCOR1	chr19:41282761-41284733	GM12878	blood:	n/a	n/a
21	BHLHE40	chr19:41283062-41284796	K562	blood:	n/a	n/a
22	MXI1	chr19:41282747-41285282	IMR90	lung:	n/a	n/a
23	POLR2A	chr19:41282921-41284953	GM12892	blood:	n/a	n/a
24	ZMIZ1	chr19:41283520-41284619	K562	blood:	n/a	n/a
25	POLR2A	chr19:41282937-41284819	GM12892	blood:	n/a	n/a
26	MAX	chr19:41283054-41284669	NB4	blood:	n/a	n/a
27	RUNX3	chr19:41282787-41284935	GM12878	blood:	n/a	n/a
28	POU2F2	chr19:41282807-41284930	GM12878	blood:	n/a	chr19:41283177-41283187 chr19:41283177-41283187 chr19:41283849-41283861 chr19:41283179-41283186 chr19:41283176-41283188 chr19:41283178-41283187 chr19:41283176-41283190 chr19:41283849-41283863 chr19:41283179-41283187 chr19:41283178-41283188 chr19:41283178-41283189 chr19:41283175-41283190 chr19:41283178-41283189
29	MYC	chr19:41283560-41284418	K562	blood:	n/a	n/a
30	NFYB	chr19:41283233-41284542	K562	blood:	n/a	chr19:41283980-41283992 chr19:41283981-41283996
31	BHLHE40	chr19:41283159-41285010	HepG2	liver:	n/a	n/a
32	MTA3	chr19:41282604-41285252	GM12878	blood:	n/a	n/a
33	TAF1	chr19:41283713-41284405	K562	blood:	n/a	n/a
34	MAFK	chr19:41283314-41285140	HepG2	liver:	n/a	n/a
35	IRF1	chr19:41283326-41284782	K562	blood:	n/a	chr19:41284581-41284595 chr19:41283567-41283580 chr19:41284139-41284153 chr19:41283983-41283992 chr19:41284359-41284373 chr19:41283999-41284013 chr19:41284381-41284395 chr19:41284050-41284064 chr19:41284600-41284614
36	USF1	chr19:41283592-41284523	A549	lung:	n/a	n/a
37	POLR2A	chr19:41283436-41284894	GM12878	blood:	n/a	n/a
38	MYC	chr19:41283031-41284408	NB4	blood:	n/a	n/a
39	EGR1	chr19:41283957-41284615	K562	blood:	n/a	chr19:41284142-41284156 chr19:41284595-41284610 chr19:41284149-41284158 chr19:41284055-41284068 chr19:41284141-41284154
40	POLR2A	chr19:41283024-41284895	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr19:41283062-41284583	A549	lung:	n/a	n/a
42	SP1	chr19:41283405-41284812	HepG2	liver:	n/a	chr19:41284001-41284013 chr19:41284602-41284611 chr19:41284139-41284151 chr19:41284383-41284392 chr19:41284360-41284369 chr19:41284381-41284393 chr19:41284378-41284392 chr19:41284052-41284064 chr19:41284359-41284371 chr19:41284002-41284016 chr19:41284382-41284392 chr19:41284601-41284611 chr19:41284002-41284012 chr19:41284383-41284392 chr19:41283866-41283875 chr19:41284003-41284012 chr19:41284053-41284062 chr19:41284356-41284370 chr19:41284007-41284014 chr19:41284002-41284011 chr19:41284382-41284391 chr19:41284600-41284612 chr19:41284600-41284612 chr19:41284052-41284064 chr19:41284602-41284611 chr19:41284361-41284370 chr19:41284002-41284012 chr19:41284053-41284067 chr19:41284001-41284012 chr19:41284601-41284611 chr19:41284181-41284195 chr19:41284001-41284013 chr19:41284136-41284150 chr19:41284360-41284370 chr19:41284140-41284149 chr19:41284359-41284371 chr19:41284381-41284393 chr19:41284139-41284151 chr19:41284597-41284611 chr19:41284382-41284392 chr19:41284002-41284011 chr19:41284054-41284063 chr19:41284601-41284610
43	RFX5	chr19:41282710-41285139	HepG2	liver:	n/a	chr19:41283514-41283523 chr19:41283511-41283525 chr19:41283651-41283660 chr19:41283510-41283525
44	YY1	chr19:41283722-41284419	HepG2	liver:	n/a	chr19:41284243-41284265 chr19:41284226-41284240 chr19:41284241-41284258 chr19:41284237-41284246 chr19:41284242-41284254 chr19:41284382-41284391 chr19:41284235-41284246 chr19:41284143-41284152
45	MAX	chr19:41283878-41284441	MCF-7	breast:	n/a	n/a
46	POLR2A	chr19:41283024-41285117	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr19:41283473-41284524	HUVEC	blood vessel:	n/a	n/a
48	TAF1	chr19:41282964-41285167	H1-hESC	embryonic stem cell:	n/a	n/a
49	RCOR1	chr19:41282952-41284694	Hela-S3	cervix:	n/a	n/a
50	TAF1	chr19:41283075-41284847	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:41284348-41284398	NHBE	bronchial:	n/a
2	chr19:41284348-41284398	AoSMC	blood vessel:	n/a
3	chr19:41284348-41284398	BE2_C	brain:	n/a
4	chr19:41284348-41284398	ProgFib	skin:	n/a
5	chr19:41284348-41284398	U87	brain:	n/a
6	chr19:41284348-41284398	PANC-1	pancreas:	n/a
7	chr19:41284348-41284398	AG09319	gingival:	n/a
8	chr19:41284348-41284398	Jurkat	blood:	n/a
9	chr19:41284348-41284398	SAEC	small airway:	n/a
10	chr19:41284348-41284398	Hepatocyte	liver:	n/a
11	chr19:41284348-41284398	SK-N-SH	brain:	n/a
12	chr19:41284348-41284398	NH-A	brain:	n/a
13	chr19:41284348-41284398	GM12878	blood:	n/a
14	chr19:41284348-41284398	AG10803	skin:	n/a
15	chr19:41284348-41284398	HEK293	kidney:	embryo
16	chr19:41284348-41284398	H1-hESC	embryonic stem cell:	embryo
17	chr19:41284348-41284398	PFSK-1	brain:	n/a
18	chr19:41284348-41284398	NB4	blood:	n/a
19	chr19:41284348-41284398	HCM	heart:	n/a
20	chr19:41284348-41284398	Caco-2	colon:	n/a
21	chr19:41284348-41284398	HPAEpiC	pulmonary alveolar:	n/a
22	chr19:41284348-41284398	IMR90	lung:	fetal
23	chr19:41284348-41284398	HIPEpiC	eye:	n/a
24	chr19:41284348-41284398	A549	lung:	n/a
25	chr19:41284348-41284398	GM12891	blood:	n/a
26	chr19:41284348-41284398	ovcar-3	ovarian:	n/a
27	chr19:41284348-41284398	HL-60	blood:	n/a
28	chr19:41284348-41284398	NHDF-neo	bronchial:	n/a
29	chr19:41284348-41284398	HAEpiC	amniotic membrane:	n/a
30	chr19:41284348-41284398	PrEC	prostate:	n/a
31	chr19:41284348-41284398	HCT-116	colon:	n/a
32	chr19:41284348-41284398	NT2-D1	testis:	n/a
33	chr19:41284348-41284398	K562	blood:	n/a
34	chr19:41284348-41284398	GM06990	blood:	n/a
35	chr19:41284348-41284398	CMK	blood:	n/a
36	chr19:41284348-41284398	T-47D	breast:	n/a
37	chr19:41284348-41284398	MCF-7	breast:	n/a
38	chr19:41284348-41284398	LNCaP	prostate:	n/a
39	chr19:41284348-41284398	HCPEpiC	choroid plexus:	n/a
40	chr19:41284348-41284398	RPTEC	kidney:	n/a
41	chr19:41284348-41284398	SK-N-MC	brain:	n/a
42	chr19:41284348-41284398	HRE	kidney:	n/a
43	chr19:41284348-41284398	HepG2	liver:	n/a
44	chr19:41284348-41284398	HEEpiC	esophagus:	n/a
45	chr19:41284348-41284398	HUVEC	blood vessel:	n/a
46	chr19:41284348-41284398	HMEC	breast:	n/a
47	chr19:41284348-41284398	Hela-S3	cervix:	n/a
48	chr19:41284348-41284398	HNPCEpiC	eye:	n/a
49	chr19:41284348-41284398	GM19239	blood:	n/a
50	chr19:41284348-41284398	BJ	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41282962..41284842-chr19:41308232..41310693,2	MCF-7	breast:
2	chr19:41195540..41197710-chr19:41283825..41285603,2	MCF-7	breast:
3	chr19:41260700..41263624-chr19:41281746..41284711,4	K562	blood:
4	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
5	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
6	chr19:41260895..41264688-chr19:41281653..41284501,3	MCF-7	breast:
7	chr19:41219466..41223288-chr19:41281896..41285456,5	MCF-7	breast:
8	chr19:41220807..41223667-chr19:41282098..41285361,4	MCF-7	breast:
9	chr19:41276921..41279823-chr19:41282678..41284570,2	MCF-7	breast:
10	chr19:41282306..41285368-chr19:41311943..41315414,5	MCF-7	breast:
11	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
12	chr19:41221538..41223321-chr19:41282786..41284711,2	K562	blood:
13	chr14:102505039..102506720-chr19:41282932..41285736,2	MCF-7	breast:
14	chr19:41282175..41285758-chr19:41311471..41315456,8	K562	blood:
15	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
16	chr19:41282692..41284743-chr19:41312820..41314498,2	MCF-7	breast:
17	chr19:41195631..41198231-chr19:41282908..41284681,3	K562	blood:
18	chr19:41283422..41285801-chr19:41305183..41308009,2	MCF-7	breast:
19	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
20	chr19:41281732..41286442-chr19:41302482..41306628,13	K562	blood:
21	chr19:41283851..41288555-chr19:41290136..41292963,4	MCF-7	breast:
22	chr19:41274845..41278396-chr19:41279079..41284996,6	K562	blood:
23	chr19:41220672..41223321-chr19:41282772..41284711,3	K562	blood:
24	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
25	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:

Variant related genes	Relation type
RAB4B	TF binding region
RAB4B-EGLN2	TF binding region
RAB4B-EGLN2	CpG island
RAB4B	CpG island
ENSG00000077312	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000197102	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13108	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17726258	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs2230694	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2233153	0.89[ASN][1000 genomes]
rs2233154	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233156	0.89[ASN][1000 genomes]
rs2233159	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249854	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545760	0.92[ASN][1000 genomes]
rs2545777	1.00[ASN][1000 genomes]
rs2545778	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2604876	0.99[ASN][1000 genomes]
rs2604877	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604909	0.95[ASN][1000 genomes]
rs2604910	0.95[ASN][1000 genomes]
rs2604911	0.95[ASN][1000 genomes]
rs2607411	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2607412	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2607413	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2607416	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2607419	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607421	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607422	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607423	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607425	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607426	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644917	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34842744	0.95[ASN][1000 genomes]
rs56891752	1.00[ASN][1000 genomes]
rs60533951	0.96[ASN][1000 genomes]
rs8107978	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109099	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[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	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv13500	chr19:41283063-41285263	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	11 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	chr19:41282800-41285000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41282800-41285200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:41282800-41285400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:41283000-41284800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr19:41283000-41285000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:41283000-41285200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr19:41283000-41285200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:41283000-41285200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:41283000-41285200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:41283000-41285400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr19:41283000-41285400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:41283000-41285400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:41283000-41285400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:41283200-41284400	Active TSS	Monocytes-CD14+_RO01746	blood
15	chr19:41283200-41284600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr19:41283200-41284600	Active TSS	Primary B cells from cord blood	blood
17	chr19:41283200-41284600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:41283200-41284600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr19:41283200-41284600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:41283200-41284600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:41283200-41284600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:41283200-41284600	Active TSS	Duodenum Mucosa	Duodenum
23	chr19:41283200-41284600	Active TSS	Esophagus	oesophagus
24	chr19:41283200-41284600	Active TSS	Fetal Intestine Small	intestine
25	chr19:41283200-41284600	Active TSS	Gastric	stomach
26	chr19:41283200-41284600	Active TSS	Pancreas	Pancrea
27	chr19:41283200-41284600	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr19:41283200-41284600	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr19:41283200-41284600	Active TSS	Rectal Smooth Muscle	rectum
30	chr19:41283200-41284600	Active TSS	Right Ventricle	heart
31	chr19:41283200-41284600	Active TSS	Small Intestine	intestine
32	chr19:41283200-41284600	Active TSS	Stomach Mucosa	stomach
33	chr19:41283200-41284800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:41283200-41284800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:41283200-41284800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:41283200-41284800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:41283200-41284800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:41283200-41284800	Active TSS	Brain Angular Gyrus	brain
39	chr19:41283200-41284800	Active TSS	Brain Hippocampus Middle	brain
40	chr19:41283200-41284800	Active TSS	Brain Substantia Nigra	brain
41	chr19:41283200-41284800	Active TSS	Colonic Mucosa	Colon
42	chr19:41283200-41284800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr19:41283200-41284800	Active TSS	Fetal Kidney	kidney
44	chr19:41283200-41284800	Active TSS	Fetal Lung	lung
45	chr19:41283200-41284800	Active TSS	Left Ventricle	heart
46	chr19:41283200-41284800	Active TSS	Right Atrium	heart
47	chr19:41283200-41284800	Active TSS	HSMMtube	muscle
48	chr19:41283200-41284800	Active TSS	NH-A	brain
49	chr19:41283200-41285000	Active TSS	H1 Cell Line	embryonic stem cell
50	chr19:41283200-41285000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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