Variant report

Variant	rs11880326
Chromosome Location	chr19:38746209-38746210
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	SIN3AK20	chr19:38746049-38746499	K562	blood:	n/a	n/a
2	SIN3A	chr19:38746204-38746218	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:38746009-38747334	K562	blood:	n/a	n/a
4	MAX	chr19:38745893-38748116	A549	lung:	n/a	chr19:38746263-38746273
5	CBX3	chr19:38745701-38746562	K562	blood:	n/a	n/a
6	MYC	chr19:38746125-38746268	K562	blood:	n/a	n/a
7	ZBTB7A	chr19:38746073-38747407	K562	blood:	n/a	n/a
8	MXI1	chr19:38746069-38746469	K562	blood:	n/a	n/a
9	MAX	chr19:38745706-38747540	K562	blood:	n/a	chr19:38746263-38746273
10	POLR2A	chr19:38745922-38747394	K562	blood:	n/a	n/a
11	HDAC2	chr19:38745722-38746443	K562	blood:	n/a	chr19:38746131-38746140
12	MYC	chr19:38745739-38747511	K562	blood:	n/a	chr19:38746263-38746273
13	TAL1	chr19:38745757-38746439	K562	blood:	n/a	n/a
14	EGR1	chr19:38746016-38746488	K562	blood:	n/a	n/a
15	EP300	chr19:38745828-38746496	K562	blood:	n/a	chr19:38746264-38746280
16	POLR2A	chr19:38746075-38747567	PANC-1	pancreas:	n/a	n/a
17	TEAD4	chr19:38745831-38746341	K562	blood:	n/a	n/a
18	KAP1	chr19:38745819-38746422	U2OS	brain:	n/a	chr19:38746153-38746162
19	MAX	chr19:38745965-38746569	K562	blood:	n/a	chr19:38746263-38746273
20	HEY1	chr19:38745971-38746556	K562	blood:	n/a	n/a
21	SIN3AK20	chr19:38746181-38747577	PANC-1	pancreas:	n/a	n/a
22	ZBTB7A	chr19:38745940-38746568	K562	blood:	n/a	n/a
23	UBTF	chr19:38746113-38747426	K562	blood:	n/a	n/a
24	JUND	chr19:38745932-38746673	K562	blood:	n/a	chr19:38746152-38746160 chr19:38746153-38746160
25	TCF12	chr19:38745828-38747706	A549	lung:	n/a	n/a
26	ZNF384	chr19:38745917-38746329	K562	blood:	n/a	n/a
27	TBL1XR1	chr19:38746021-38746347	K562	blood:	n/a	n/a
28	POLR2A	chr19:38745805-38746632	K562	blood:	n/a	n/a
29	SIX5	chr19:38746035-38747596	A549	lung:	n/a	n/a
30	BHLHE40	chr19:38745759-38747480	K562	blood:	n/a	n/a
31	RCOR1	chr19:38745715-38747490	K562	blood:	n/a	n/a
32	YY1	chr19:38746053-38746492	K562	blood:	n/a	chr19:38746266-38746277
33	E2F4	chr19:38746069-38747486	K562	blood:	n/a	chr19:38747066-38747075 chr19:38746997-38747007 chr19:38746270-38746280 chr19:38747345-38747354
34	EP300	chr19:38746093-38746392	K562	blood:	n/a	chr19:38746264-38746280
35	HMGN3	chr19:38746116-38746333	K562	blood:	n/a	n/a
36	E2F6	chr19:38746050-38747415	K562	blood:	n/a	chr19:38747066-38747075 chr19:38746997-38747007 chr19:38746270-38746280 chr19:38747345-38747354
37	CEBPB	chr19:38745650-38746311	K562	blood:	n/a	n/a
38	POLR2A	chr19:38745912-38747557	PANC-1	pancreas:	n/a	n/a
39	NR2F2	chr19:38745636-38746541	K562	blood:	n/a	n/a
40	ELF1	chr19:38746146-38746407	K562	blood:	n/a	n/a
41	TAF1	chr19:38745989-38746403	K562	blood:	n/a	n/a
42	TBP	chr19:38745999-38746520	K562	blood:	n/a	n/a
43	EGR1	chr19:38745766-38746515	K562	blood:	n/a	n/a
44	RAD21	chr19:38746128-38746310	K562	blood:	n/a	n/a
45	MAZ	chr19:38745893-38747511	K562	blood:	n/a	chr19:38746263-38746273
46	NR2F2	chr19:38745581-38746562	K562	blood:	n/a	n/a
47	CTCF	chr19:38746063-38746245	K562	blood:	n/a	n/a
48	JUN	chr19:38745741-38747679	K562	blood:	n/a	chr19:38746152-38746160 chr19:38746153-38746160
49	MAX	chr19:38745993-38747565	A549	lung:	n/a	chr19:38746263-38746273
50	POLR2A	chr19:38746092-38747343	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38745286..38748830-chr19:38824490..38828580,5	K562	blood:
2	chr19:38745470..38748025-chr19:38806544..38809528,4	K562	blood:
3	chr19:38745341..38747261-chr19:38850863..38853246,2	K562	blood:
4	chr19:38744771..38747370-chr19:38793659..38796631,3	MCF-7	breast:
5	chr19:38744545..38747881-chr19:38796739..38799856,3	K562	blood:
6	chr19:38745311..38747028-chr19:38754181..38756021,2	MCF-7	breast:
7	chr19:38746183..38748575-chr19:38806704..38809483,2	K562	blood:

Variant related genes	Relation type
PPP1R14A	TF binding region
ENSG00000167645	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167644	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10993	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880301	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880459	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745948	0.88[ASN][1000 genomes]
rs59648079	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60163114	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508780	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249532	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253827	0.82[EUR][1000 genomes]
rs7260295	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030309	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030311	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101482	0.91[ASN][1000 genomes]
rs8111378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112201	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38743000-38746400	Weak transcription	HUVEC	blood vessel
2	chr19:38744000-38746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:38744200-38746400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:38744200-38746400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:38744600-38746400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:38744600-38746400	Weak transcription	NHEK	skin
7	chr19:38744600-38746600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:38744800-38746400	Weak transcription	Gastric	stomach
9	chr19:38744800-38747200	Active TSS	Colon Smooth Muscle	Colon
10	chr19:38744800-38747400	Active TSS	Aorta	Aorta
11	chr19:38744800-38747600	Active TSS	Brain Anterior Caudate	brain
12	chr19:38744800-38747600	Active TSS	Brain Cingulate Gyrus	brain
13	chr19:38745000-38747400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr19:38745000-38747400	Active TSS	Brain Substantia Nigra	brain
15	chr19:38745000-38747400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
16	chr19:38745000-38747600	Active TSS	Brain Angular Gyrus	brain
17	chr19:38745200-38746800	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr19:38745400-38747400	Active TSS	Rectal Smooth Muscle	rectum
19	chr19:38745600-38747000	Active TSS	Brain Hippocampus Middle	brain
20	chr19:38745800-38746400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:38745800-38746400	Active TSS	Placenta	Placenta
22	chr19:38745800-38746400	Active TSS	Right Atrium	heart
23	chr19:38745800-38746600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:38745800-38746600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr19:38745800-38746600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr19:38745800-38746600	Active TSS	Colonic Mucosa	Colon
27	chr19:38745800-38746600	Active TSS	Lung	lung
28	chr19:38745800-38746600	Active TSS	Pancreas	Pancrea
29	chr19:38745800-38746800	Enhancers	Primary hematopoietic stem cells	blood
30	chr19:38745800-38746800	Active TSS	Esophagus	oesophagus
31	chr19:38745800-38746800	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr19:38745800-38746800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr19:38745800-38747000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr19:38745800-38747200	Active TSS	NHLF	lung
35	chr19:38745800-38747400	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr19:38745800-38747400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:38745800-38747400	Active TSS	Left Ventricle	heart
38	chr19:38745800-38747400	Active TSS	Psoas Muscle	Psoas
39	chr19:38745800-38747400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr19:38745800-38747600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:38745800-38747600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr19:38746000-38746400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
43	chr19:38746000-38746400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:38746000-38746600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
45	chr19:38746000-38746600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr19:38746000-38746600	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr19:38746000-38746600	Flanking Active TSS	A549	lung
48	chr19:38746000-38746800	Active TSS	Liver	Liver
49	chr19:38746000-38746800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr19:38746000-38746800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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