Variant report

Variant	rs8101485
Chromosome Location	chr19:38719302-38719303
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	REST	chr19:38719009-38719841	H1-neurons	neurons:	n/a	chr19:38719471-38719484
2	CHD2	chr19:38718807-38719471	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr19:38719054-38719672	H1-neurons	neurons:	n/a	n/a
4	MAX	chr19:38718543-38719486	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF263	chr19:38719255-38719581	HEK293-T-REx	kidney:	n/a	chr19:38719371-38719392
6	TCF7L2	chr19:38719064-38719881	HCT-116	colon:	n/a	n/a
7	POLR2A	chr19:38718559-38720966	H1-neurons	neurons:	n/a	n/a
8	MAX	chr19:38718603-38719545	H1-hESC	embryonic stem cell:	n/a	n/a
9	NR3C1	chr19:38718917-38719662	A549	lung:	n/a	chr19:38719588-38719601
10	SP1	chr19:38719032-38719492	H1-hESC	embryonic stem cell:	n/a	chr19:38719128-38719135 chr19:38719178-38719192 chr19:38719102-38719116 chr19:38719158-38719172 chr19:38719187-38719199 chr19:38719280-38719291 chr19:38719222-38719233 chr19:38719281-38719290 chr19:38719188-38719197 chr19:38719184-38719198 chr19:38719097-38719111
11	REST	chr19:38718508-38721161	H1-neurons	neurons:	n/a	chr19:38718827-38718837 chr19:38719471-38719484 chr19:38718636-38718649 chr19:38720543-38720556
12	POLR2A	chr19:38718631-38720930	H1-neurons	neurons:	n/a	n/a
13	ELF1	chr19:38719200-38719537	K562	blood:	n/a	n/a
14	TBL1XR1	chr19:38719250-38719359	K562	blood:	n/a	n/a
15	TCF12	chr19:38719116-38719453	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZBTB7A	chr19:38719247-38719415	K562	blood:	n/a	n/a
17	TCF12	chr19:38719056-38719366	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZBTB7A	chr19:38719286-38720226	ECC-1	luminal epithelium:	n/a	chr19:38720079-38720087 chr19:38720078-38720086
19	POLR2A	chr19:38718387-38719440	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr19:38719067-38719464	H1-hESC	embryonic stem cell:	n/a	chr19:38719121-38719132 chr19:38719281-38719292 chr19:38719188-38719199
21	SIN3AK20	chr19:38719065-38719699	H1-hESC	embryonic stem cell:	n/a	n/a
22	SIN3A	chr19:38718309-38720711	H1-hESC	embryonic stem cell:	n/a	chr19:38718770-38718781
23	TCF12	chr19:38719112-38719958	A549	lung:	n/a	n/a
24	E2F6	chr19:38718577-38719554	H1-hESC	embryonic stem cell:	n/a	chr19:38719223-38719235
25	SIN3AK20	chr19:38719047-38720071	PANC-1	pancreas:	n/a	n/a
26	JUND	chr19:38719047-38719343	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAZ	chr19:38719170-38719385	K562	blood:	n/a	n/a
28	SIN3AK20	chr19:38719059-38719430	SK-N-SH	brain:	n/a	n/a
29	TBP	chr19:38719190-38719452	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTBP2	chr19:38719154-38720005	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr19:38719093-38720928	IMR90	lung:	n/a	chr19:38720133-38720143 chr19:38719671-38719681
32	ZNF143	chr19:38719235-38719503	H1-hESC	embryonic stem cell:	n/a	chr19:38719290-38719308
33	SIN3AK20	chr19:38719200-38719509	PANC-1	pancreas:	n/a	n/a
34	MXI1	chr19:38718532-38721022	SK-N-SH	brain:	n/a	n/a
35	E2F6	chr19:38719090-38719334	K562	blood:	n/a	chr19:38719223-38719235
36	NANOG	chr19:38719014-38719341	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr19:38719096-38719651	A549	lung:	n/a	n/a
38	MAX	chr19:38719096-38719783	A549	lung:	n/a	chr19:38719671-38719681
39	TAF1	chr19:38719045-38720842	H1-neurons	neurons:	n/a	n/a
40	MAX	chr19:38719074-38719396	K562	blood:	n/a	n/a
41	ELF1	chr19:38719207-38719558	K562	blood:	n/a	n/a
42	ELF1	chr19:38719187-38719735	GM12878	blood:	n/a	n/a
43	MYC	chr19:38719233-38719426	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38718052..38720655-chr19:38755234..38758069,2	MCF-7	breast:
2	chr19:38711348..38714655-chr19:38718716..38721513,3	MCF-7	breast:
3	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
4	chr19:38705043..38707659-chr19:38719005..38721797,2	K562	blood:
5	chr19:38718989..38720789-chr19:38865301..38866855,2	MCF-7	breast:
6	chr19:38715608..38719883-chr19:38825304..38828918,6	K562	blood:
7	chr19:38713729..38715404-chr19:38717530..38720413,2	K562	blood:
8	chr19:38717810..38720228-chr19:38876711..38878921,2	K562	blood:

Variant related genes	Relation type
DPF1	TF binding region
ENSG00000011332	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000179168	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2384781	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60328056	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256364	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8108197	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109991	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3437908	chr19:38717937-38720485	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3440033	chr19:38718162-38720160	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv3419802	chr19:38718712-38720860	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	esv3405182	chr19:38719137-38721685	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8101485	SPINT2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38715600-38719400	Weak transcription	Brain Anterior Caudate	brain
2	chr19:38715600-38719600	Weak transcription	Hela-S3	cervix
3	chr19:38716600-38720800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr19:38717600-38719400	Weak transcription	K562	blood
5	chr19:38718000-38720800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:38718200-38720000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
7	chr19:38718400-38719600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr19:38718400-38719600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:38718400-38720600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr19:38718400-38721000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:38718600-38719400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr19:38718600-38719400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:38718600-38719400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr19:38718600-38719400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:38718600-38719800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
16	chr19:38718600-38719800	Bivalent Enhancer	Fetal Thymus	thymus
17	chr19:38718600-38720000	Bivalent Enhancer	Primary T cells from cord blood	blood
18	chr19:38718600-38720200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:38718600-38720600	Active TSS	Brain Angular Gyrus	brain
20	chr19:38718600-38720600	Active TSS	Right Ventricle	heart
21	chr19:38718600-38720800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr19:38718800-38719400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr19:38718800-38719800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:38718800-38720000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr19:38718800-38720200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:38718800-38720600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:38718800-38720600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:38718800-38720800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr19:38718800-38720800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:38718800-38720800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:38718800-38721000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:38718800-38721000	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr19:38718800-38721200	Active TSS	Brain Germinal Matrix	brain
34	chr19:38718800-38721200	Active TSS	Fetal Brain Female	brain
35	chr19:38719000-38719400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:38719000-38719800	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr19:38719000-38719800	Bivalent Enhancer	Small Intestine	intestine
38	chr19:38719000-38720000	Enhancers	Fetal Heart	heart
39	chr19:38719000-38720600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr19:38719000-38720600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:38719000-38720600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:38719000-38720600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:38719000-38720600	Active TSS	Right Atrium	heart
44	chr19:38719200-38719400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:38719200-38719400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:38719200-38719400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:38719200-38719400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:38719200-38719400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:38719200-38719400	Active TSS	Muscle Satellite Cultured Cells	--
50	chr19:38719200-38719400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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