Variant report

Variant	rs2384781
Chromosome Location	chr19:38719007-38719008
allele	A/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	CHD2	chr19:38718807-38719471	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:38718543-38719486	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB7A	chr19:38718749-38719238	K562	blood:	n/a	n/a
4	E2F6	chr19:38718611-38719178	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:38718559-38720966	H1-neurons	neurons:	n/a	n/a
6	MAX	chr19:38718603-38719545	H1-hESC	embryonic stem cell:	n/a	n/a
7	NR3C1	chr19:38718917-38719662	A549	lung:	n/a	chr19:38719588-38719601
8	REST	chr19:38718508-38721161	H1-neurons	neurons:	n/a	chr19:38718827-38718837 chr19:38719471-38719484 chr19:38718636-38718649 chr19:38720543-38720556
9	POLR2A	chr19:38718631-38720930	H1-neurons	neurons:	n/a	n/a
10	ZBTB7A	chr19:38718439-38719034	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr19:38718413-38719021	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:38718387-38719440	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr19:38718309-38720711	H1-hESC	embryonic stem cell:	n/a	chr19:38718770-38718781
14	E2F6	chr19:38718577-38719554	H1-hESC	embryonic stem cell:	n/a	chr19:38719223-38719235
15	MXI1	chr19:38718532-38721022	SK-N-SH	brain:	n/a	n/a
16	SP1	chr19:38718527-38719013	H1-hESC	embryonic stem cell:	n/a	chr19:38718998-38719012 chr19:38718996-38719006

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	chr19:38713729..38715323-chr19:38716058..38719030,2	K562	blood:
4	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
5	chr19:38705043..38707659-chr19:38719005..38721797,2	K562	blood:
6	chr19:38718989..38720789-chr19:38865301..38866855,2	MCF-7	breast:
7	chr19:38715608..38719883-chr19:38825304..38828918,6	K562	blood:
8	chr19:38713729..38715404-chr19:38717530..38720413,2	K562	blood:
9	chr19:38717810..38720228-chr19:38876711..38878921,2	K562	blood:

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

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs60328056	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7253360	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7253473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7256364	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8101485	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8108197	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109991	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2384781	SPINT2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38715200-38719200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:38715200-38719200	Weak transcription	Pancreas	Pancrea
3	chr19:38715400-38719200	Weak transcription	NH-A	brain
4	chr19:38715400-38719200	Weak transcription	NHDF-Ad	bronchial
5	chr19:38715600-38719400	Weak transcription	Brain Anterior Caudate	brain
6	chr19:38715600-38719600	Weak transcription	Hela-S3	cervix
7	chr19:38716600-38719200	Enhancers	A549	lung
8	chr19:38716600-38720800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr19:38716800-38719200	Enhancers	Fetal Brain Male	brain
10	chr19:38717400-38719200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:38717600-38719400	Weak transcription	K562	blood
12	chr19:38718000-38720800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:38718200-38720000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
14	chr19:38718400-38719600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr19:38718400-38719600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:38718400-38720600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr19:38718400-38721000	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:38718600-38719200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:38718600-38719200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:38718600-38719200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr19:38718600-38719200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr19:38718600-38719200	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr19:38718600-38719200	Bivalent Enhancer	Fetal Stomach	stomach
24	chr19:38718600-38719400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
25	chr19:38718600-38719400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:38718600-38719400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
27	chr19:38718600-38719400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:38718600-38719800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
29	chr19:38718600-38719800	Bivalent Enhancer	Fetal Thymus	thymus
30	chr19:38718600-38720000	Bivalent Enhancer	Primary T cells from cord blood	blood
31	chr19:38718600-38720200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:38718600-38720600	Active TSS	Brain Angular Gyrus	brain
33	chr19:38718600-38720600	Active TSS	Right Ventricle	heart
34	chr19:38718600-38720800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr19:38718800-38719200	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr19:38718800-38719200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:38718800-38719400	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr19:38718800-38719800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr19:38718800-38720000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:38718800-38720200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:38718800-38720600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:38718800-38720600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:38718800-38720800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr19:38718800-38720800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr19:38718800-38720800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr19:38718800-38721000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:38718800-38721000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr19:38718800-38721200	Active TSS	Brain Germinal Matrix	brain
49	chr19:38718800-38721200	Active TSS	Fetal Brain Female	brain
50	chr19:38719000-38719200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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