Variant report

Variant	rs73030000
Chromosome Location	chr19:35768155-35768156
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	POLR2A	chr19:35768117-35768293	K562	blood:	n/a	n/a
2	POLR2A	chr19:35767911-35768387	K562	blood:	n/a	n/a
3	POLR2A	chr19:35768128-35768442	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:35768123-35768424	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:35768114-35768453	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:35768155-35768881	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:35767936-35768426	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:35767549-35768885	K562	blood:	n/a	n/a
9	POLR2A	chr19:35768096-35768799	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:35768050-35768631	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:35767703-35768436	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:35767956-35768347	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:35758518..35761825-chr19:35766786..35769886,4	K562	blood:

Variant related genes	Relation type
HAMP	TF binding region
USF2	TF binding region
ENSG00000105698	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16970163	0.81[ASN][1000 genomes]
rs34259399	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55850007	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56138958	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs569596	0.80[AMR][1000 genomes]
rs7248140	0.81[ASN][1000 genomes]
rs73029989	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8100411	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
9	nsv911619	chr19:35749563-35775441	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
10	nsv911620	chr19:35752917-35771382	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
11	nsv911621	chr19:35752917-35772471	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
12	nsv911622	chr19:35752917-35773146	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
13	nsv911623	chr19:35752917-35775441	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
14	nsv911624	chr19:35759043-35771382	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73030000	LGI4	cis	cerebellar cortex	BrainEAC

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35761000-35770400	Weak transcription	HSMM	muscle
2	chr19:35761200-35770200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:35761200-35770400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:35761200-35770400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:35761200-35770600	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:35761200-35772200	Weak transcription	Psoas Muscle	Psoas
7	chr19:35761400-35768200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:35761400-35768200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:35761400-35769200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:35761400-35769800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:35761400-35770000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:35761400-35770200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr19:35761400-35770200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:35761400-35770200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:35761400-35770400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:35761400-35770400	Strong transcription	Rectal Smooth Muscle	rectum
17	chr19:35761400-35770600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:35761400-35770800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:35761400-35770800	Strong transcription	Fetal Thymus	thymus
20	chr19:35761400-35771000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:35761400-35771000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:35761400-35771000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:35761400-35771000	Strong transcription	Brain Germinal Matrix	brain
24	chr19:35761400-35771200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:35761400-35772000	Strong transcription	Fetal Stomach	stomach
26	chr19:35761400-35775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:35761600-35768600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:35761600-35770000	Strong transcription	Primary T cells from cord blood	blood
29	chr19:35761600-35770400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr19:35761600-35770600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:35761600-35770600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:35761600-35771000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:35761600-35771000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:35761600-35771000	Strong transcription	Fetal Intestine Large	intestine
35	chr19:35761600-35771000	Strong transcription	Thymus	Thymus
36	chr19:35761600-35771200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:35761600-35771400	Strong transcription	Fetal Intestine Small	intestine
38	chr19:35761600-35771400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:35761800-35768400	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:35761800-35769600	Weak transcription	Fetal Brain Male	brain
41	chr19:35761800-35770200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr19:35761800-35770600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:35761800-35770800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr19:35761800-35771000	Strong transcription	Fetal Brain Female	brain
45	chr19:35762000-35770600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr19:35762200-35771200	Strong transcription	Right Ventricle	heart
47	chr19:35762400-35772000	Weak transcription	K562	blood
48	chr19:35762800-35768200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:35762800-35770200	Strong transcription	Dnd41	blood
50	chr19:35762800-35772000	Weak transcription	Stomach Mucosa	stomach

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