Variant report

Variant	rs2388247
Chromosome Location	chr13:30426353-30426354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30424847..30426719-chr13:30430833..30432673,4	MCF-7	breast:
2	chr13:30421278..30427133-chr13:30682148..30691157,22	MCF-7	breast:
3	chr13:30420595..30432624-chr13:30489594..30503683,39	MCF-7	breast:
4	chr13:30425761..30427408-chr13:30430523..30432297,2	MCF-7	breast:
5	chr13:30422516..30424271-chr13:30426326..30429271,2	K562	blood:

Variant related genes	Relation type
ENSG00000224405	Chromatin interaction
ENSG00000224511	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1058650	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[ASN][1000 genomes]
rs11147398	0.80[ASN][1000 genomes]
rs12872400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1323931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1410110	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2025604	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234416	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.82[ASN][1000 genomes]
rs2388246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2761938	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2761939	0.83[ASN][1000 genomes]
rs2761940	0.85[ASN][1000 genomes]
rs278034	0.88[ASN][1000 genomes]
rs278049	0.82[CHB][hapmap]
rs35541102	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4083610	0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4238128	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs4265673	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4297554	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4769775	0.80[ASN][1000 genomes]
rs6490429	0.81[ASN][1000 genomes]
rs6490430	0.81[ASN][1000 genomes]
rs7320474	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7326253	0.81[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7330356	0.82[CHB][hapmap]
rs7335148	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs765404	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7981622	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7995666	0.91[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9314978	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9506226	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9506229	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9506231	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9506233	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9508553	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9508554	0.85[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9508557	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508558	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508559	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9508560	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9508561	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9508564	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508568	0.85[ASN][1000 genomes]
rs9550494	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9551741	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9551744	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9551751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9551753	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9578136	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs9578139	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription 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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30424800-30426400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:30424800-30426600	Weak transcription	Psoas Muscle	Psoas
3	chr13:30424800-30426600	Weak transcription	Right Atrium	heart
4	chr13:30424800-30427600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:30424800-30429600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:30425200-30426400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:30425200-30426400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:30425200-30426400	Weak transcription	Adipose Nuclei	Adipose
9	chr13:30425200-30426600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:30425200-30426600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr13:30425200-30426600	Weak transcription	HSMMtube	muscle
12	chr13:30425200-30426600	Weak transcription	NHLF	lung
13	chr13:30425200-30426800	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:30425200-30427600	Enhancers	A549	lung
15	chr13:30425200-30428400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:30425200-30429600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:30425200-30429800	Weak transcription	Fetal Intestine Small	intestine
18	chr13:30425200-30429800	Weak transcription	Pancreas	Pancrea
19	chr13:30425200-30430000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr13:30425200-30430200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:30425200-30430200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr13:30425400-30426400	Weak transcription	NHDF-Ad	bronchial
23	chr13:30425400-30426400	Weak transcription	Osteobl	bone
24	chr13:30425400-30426600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:30425400-30426600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:30425400-30426600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:30425400-30426800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:30425400-30426800	Weak transcription	NH-A	brain
29	chr13:30425400-30428600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr13:30425400-30429600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:30425400-30429800	Weak transcription	Fetal Lung	lung
32	chr13:30425400-30429800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:30425400-30429800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:30425400-30430000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:30425400-30430000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:30425400-30430000	Weak transcription	Stomach Mucosa	stomach
37	chr13:30425400-30430200	Weak transcription	Fetal Kidney	kidney
38	chr13:30425600-30426600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr13:30425600-30429800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr13:30425600-30429800	Weak transcription	Hela-S3	cervix
41	chr13:30425800-30427200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:30426000-30427400	Enhancers	HSMM	muscle
43	chr13:30426000-30427800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:30426200-30427600	Enhancers	Placenta Amnion	Placenta Amnion

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