Variant report

Variant	rs2599447
Chromosome Location	chr19:44007012-44007013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:43997566..43999974-chr19:44006795..44009700,2	K562	blood:
2	chr19:43977180..43982299-chr19:44003653..44008245,6	K562	blood:
3	chr19:43997566..43999110-chr19:44006795..44008578,2	K562	blood:
4	chr19:43967204..43969877-chr19:44006593..44010322,9	MCF-7	breast:
5	chr19:44006496..44008143-chr19:44098024..44100658,2	MCF-7	breast:
6	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:
7	chr19:44005750..44008125-chr19:44129589..44132282,2	K562	blood:
8	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
9	chr19:44006689..44009864-chr19:44027261..44031051,4	MCF-7	breast:
10	chr19:43967644..43971432-chr19:44003665..44007669,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105767	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000124466	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1125030	0.86[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs12978269	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1799778	0.88[JPT][hapmap]
rs2203990	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2256507	0.88[JPT][hapmap]
rs2261316	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2305375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2355994	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs25486	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs25487	0.88[JPT][hapmap]
rs2599435	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs2599440	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2599445	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2599454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2599455	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2599456	0.87[EUR][1000 genomes]
rs2682543	0.84[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs2682549	0.86[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs2682553	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682566	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2682578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682579	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810378	0.88[JPT][hapmap]
rs6509092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs6509096	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7252955	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv2762041	chr19:43986023-44014457	Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2599447	SLC8A2	cis	cerebellum	SCAN
rs2599447	SLC17A7	cis	cerebellum	SCAN
rs2599447	BCAT2	cis	cerebellum	SCAN
rs2599447	IZUMO1	cis	cerebellum	SCAN
rs2599447	TEAD2	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43980800-44007400	Weak transcription	HSMM	muscle
2	chr19:43981200-44007200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:43981400-44007200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:43993000-44007200	Weak transcription	A549	lung
5	chr19:43993600-44007400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:43994200-44007200	Weak transcription	Primary B cells from cord blood	blood
7	chr19:43998000-44007200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:43999600-44007600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:43999800-44007600	Weak transcription	HSMMtube	muscle
10	chr19:44000000-44007200	Weak transcription	Adipose Nuclei	Adipose
11	chr19:44000000-44007400	Weak transcription	Brain Angular Gyrus	brain
12	chr19:44000000-44008000	Weak transcription	Small Intestine	intestine
13	chr19:44001400-44007200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:44001400-44007600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:44001600-44007400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr19:44001800-44007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:44002000-44007200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:44002000-44007400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:44002000-44007800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:44002400-44007600	Weak transcription	Aorta	Aorta
21	chr19:44003200-44007200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:44003600-44007400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr19:44003600-44007600	Weak transcription	Left Ventricle	heart
24	chr19:44003600-44007600	Weak transcription	Right Atrium	heart
25	chr19:44003800-44007200	Weak transcription	Stomach Mucosa	stomach
26	chr19:44005600-44007200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:44005600-44007200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr19:44005800-44007200	Enhancers	Stomach Smooth Muscle	stomach
29	chr19:44005800-44007600	Enhancers	Pancreas	Pancrea
30	chr19:44005800-44007800	Enhancers	Spleen	Spleen
31	chr19:44006000-44007200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:44006000-44007200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:44006000-44007400	Bivalent Enhancer	Fetal Lung	lung
34	chr19:44006000-44007400	Enhancers	Placenta	Placenta
35	chr19:44006000-44008200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr19:44006200-44007200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:44006200-44007200	Enhancers	GM12878-XiMat	blood
38	chr19:44006200-44007400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr19:44006200-44007400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:44006200-44007400	Enhancers	Fetal Thymus	thymus
41	chr19:44006200-44008600	Active TSS	Colonic Mucosa	Colon
42	chr19:44006400-44007200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:44006400-44007200	Enhancers	Fetal Intestine Large	intestine
44	chr19:44006400-44007400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:44006400-44007400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr19:44006400-44007400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr19:44006400-44007600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:44006400-44007800	Enhancers	Fetal Heart	heart
49	chr19:44006400-44007800	Weak transcription	Gastric	stomach
50	chr19:44006600-44007200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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