Variant report

Variant	rs11880301
Chromosome Location	chr19:38746119-38746120
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	POLR2A	chr19:38746009-38747334	K562	blood:	n/a	n/a
3	MAX	chr19:38745893-38748116	A549	lung:	n/a	chr19:38746263-38746273
4	CBX3	chr19:38745701-38746562	K562	blood:	n/a	n/a
5	MAFK	chr19:38746098-38746190	K562	blood:	n/a	n/a
6	ZBTB7A	chr19:38746073-38747407	K562	blood:	n/a	n/a
7	MXI1	chr19:38746069-38746469	K562	blood:	n/a	n/a
8	MAX	chr19:38745706-38747540	K562	blood:	n/a	chr19:38746263-38746273
9	POLR2A	chr19:38745922-38747394	K562	blood:	n/a	n/a
10	HDAC2	chr19:38745722-38746443	K562	blood:	n/a	chr19:38746131-38746140
11	MYC	chr19:38745739-38747511	K562	blood:	n/a	chr19:38746263-38746273
12	TAL1	chr19:38745757-38746439	K562	blood:	n/a	n/a
13	EGR1	chr19:38746016-38746488	K562	blood:	n/a	n/a
14	EP300	chr19:38745828-38746496	K562	blood:	n/a	chr19:38746264-38746280
15	POLR2A	chr19:38746075-38747567	PANC-1	pancreas:	n/a	n/a
16	TEAD4	chr19:38745831-38746341	K562	blood:	n/a	n/a
17	KAP1	chr19:38745819-38746422	U2OS	brain:	n/a	chr19:38746153-38746162
18	MAX	chr19:38745965-38746569	K562	blood:	n/a	chr19:38746263-38746273
19	HEY1	chr19:38745971-38746556	K562	blood:	n/a	n/a
20	ZBTB7A	chr19:38745940-38746568	K562	blood:	n/a	n/a
21	UBTF	chr19:38746113-38747426	K562	blood:	n/a	n/a
22	JUND	chr19:38745932-38746673	K562	blood:	n/a	chr19:38746152-38746160 chr19:38746153-38746160
23	TCF12	chr19:38745828-38747706	A549	lung:	n/a	n/a
24	ZNF384	chr19:38745917-38746329	K562	blood:	n/a	n/a
25	TBL1XR1	chr19:38746021-38746347	K562	blood:	n/a	n/a
26	POLR2A	chr19:38745805-38746632	K562	blood:	n/a	n/a
27	SIX5	chr19:38746035-38747596	A549	lung:	n/a	n/a
28	MYC	chr19:38746107-38746122	K562	blood:	n/a	n/a
29	BHLHE40	chr19:38745759-38747480	K562	blood:	n/a	n/a
30	RCOR1	chr19:38745715-38747490	K562	blood:	n/a	n/a
31	YY1	chr19:38746053-38746492	K562	blood:	n/a	chr19:38746266-38746277
32	E2F4	chr19:38746069-38747486	K562	blood:	n/a	chr19:38747066-38747075 chr19:38746997-38747007 chr19:38746270-38746280 chr19:38747345-38747354
33	EP300	chr19:38746093-38746392	K562	blood:	n/a	chr19:38746264-38746280
34	HMGN3	chr19:38746116-38746333	K562	blood:	n/a	n/a
35	E2F6	chr19:38746050-38747415	K562	blood:	n/a	chr19:38747066-38747075 chr19:38746997-38747007 chr19:38746270-38746280 chr19:38747345-38747354
36	CEBPB	chr19:38745650-38746311	K562	blood:	n/a	n/a
37	POLR2A	chr19:38745912-38747557	PANC-1	pancreas:	n/a	n/a
38	NR2F2	chr19:38745636-38746541	K562	blood:	n/a	n/a
39	TAF1	chr19:38745989-38746403	K562	blood:	n/a	n/a
40	TBP	chr19:38745999-38746520	K562	blood:	n/a	n/a
41	EGR1	chr19:38745766-38746515	K562	blood:	n/a	n/a
42	RCOR1	chr19:38745764-38746202	K562	blood:	n/a	n/a
43	MAZ	chr19:38745893-38747511	K562	blood:	n/a	chr19:38746263-38746273
44	NR2F2	chr19:38745581-38746562	K562	blood:	n/a	n/a
45	CTCF	chr19:38746063-38746245	K562	blood:	n/a	n/a
46	JUN	chr19:38745741-38747679	K562	blood:	n/a	chr19:38746152-38746160 chr19:38746153-38746160
47	MAX	chr19:38745993-38747565	A549	lung:	n/a	chr19:38746263-38746273
48	POLR2A	chr19:38746092-38747343	K562	blood:	n/a	n/a
49	TBL1XR1	chr19:38745826-38746632	K562	blood:	n/a	n/a
50	MAX	chr19:38745916-38747462	K562	blood:	n/a	chr19:38746263-38746273

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	chr19:38737395..38740237-chr19:38744694..38746196,2	MCF-7	breast:
5	chr19:38744771..38747370-chr19:38793659..38796631,3	MCF-7	breast:
6	chr19:38744545..38747881-chr19:38796739..38799856,3	K562	blood:
7	chr19:38745311..38747028-chr19:38754181..38756021,2	MCF-7	breast:

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

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083454	0.82[CEU][hapmap]
rs11538289	1.00[CEU][hapmap]
rs11880326	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880459	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745948	0.86[ASN][1000 genomes]
rs3760884	1.00[CEU][hapmap]
rs59648079	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60163114	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508780	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7246386	0.85[AMR][1000 genomes]
rs7248540	1.00[CEU][hapmap]
rs7248780	1.00[CEU][hapmap]
rs7249532	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253827	0.82[EUR][1000 genomes]
rs7257976	1.00[CEU][hapmap]
rs7260295	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73030303	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73030307	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73030308	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73030309	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73030311	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101482	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs8108440	1.00[CEU][hapmap]
rs8109713	1.00[CEU][hapmap]
rs8111378	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8112201	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8112499	1.00[CEU][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11880301	SPINT2	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 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	chr19:38744400-38746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:38744600-38746200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:38744600-38746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:38744600-38746400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:38744600-38746400	Weak transcription	NHEK	skin
10	chr19:38744600-38746600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:38744800-38746200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:38744800-38746200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:38744800-38746200	Weak transcription	HMEC	breast
14	chr19:38744800-38746200	Weak transcription	HSMM	muscle
15	chr19:38744800-38746200	Weak transcription	HSMMtube	muscle
16	chr19:38744800-38746200	Weak transcription	NH-A	brain
17	chr19:38744800-38746400	Weak transcription	Gastric	stomach
18	chr19:38744800-38747200	Active TSS	Colon Smooth Muscle	Colon
19	chr19:38744800-38747400	Active TSS	Aorta	Aorta
20	chr19:38744800-38747600	Active TSS	Brain Anterior Caudate	brain
21	chr19:38744800-38747600	Active TSS	Brain Cingulate Gyrus	brain
22	chr19:38745000-38746200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:38745000-38747400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr19:38745000-38747400	Active TSS	Brain Substantia Nigra	brain
25	chr19:38745000-38747400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
26	chr19:38745000-38747600	Active TSS	Brain Angular Gyrus	brain
27	chr19:38745200-38746800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:38745400-38747400	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:38745600-38746200	Flanking Active TSS	Ovary	ovary
30	chr19:38745600-38747000	Active TSS	Brain Hippocampus Middle	brain
31	chr19:38745800-38746200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:38745800-38746200	Flanking Active TSS	Fetal Lung	lung
33	chr19:38745800-38746200	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr19:38745800-38746200	Active TSS	Right Ventricle	heart
35	chr19:38745800-38746200	Enhancers	Spleen	Spleen
36	chr19:38745800-38746200	Flanking Active TSS	K562	blood
37	chr19:38745800-38746400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:38745800-38746400	Active TSS	Placenta	Placenta
39	chr19:38745800-38746400	Active TSS	Right Atrium	heart
40	chr19:38745800-38746600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:38745800-38746600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:38745800-38746600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr19:38745800-38746600	Active TSS	Colonic Mucosa	Colon
44	chr19:38745800-38746600	Active TSS	Lung	lung
45	chr19:38745800-38746600	Active TSS	Pancreas	Pancrea
46	chr19:38745800-38746800	Enhancers	Primary hematopoietic stem cells	blood
47	chr19:38745800-38746800	Active TSS	Esophagus	oesophagus
48	chr19:38745800-38746800	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr19:38745800-38746800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr19:38745800-38747000	Flanking Active TSS	Adipose Nuclei	Adipose

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