Variant report

Variant	rs2388246
Chromosome Location	chr13:30414943-30414944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30414278..30417559-chr13:30423069..30425308,6	MCF-7	breast:
2	chr13:30410070..30411618-chr13:30413618..30415237,2	MCF-7	breast:
3	chr13:30413488..30415848-chr13:30648656..30650250,2	MCF-7	breast:
4	chr13:30414305..30417482-chr13:30498003..30500774,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1058650	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11147398	0.83[ASN][1000 genomes]
rs12872400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1323931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1410110	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2025604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234416	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2388247	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];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2761939	0.86[ASN][1000 genomes]
rs2761940	0.88[ASN][1000 genomes]
rs278034	0.91[ASN][1000 genomes]
rs278049	0.83[CHB][hapmap]
rs35541102	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4083610	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4238128	0.87[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4265673	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4297554	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4769775	0.83[ASN][1000 genomes]
rs6490429	0.84[ASN][1000 genomes]
rs6490430	0.84[ASN][1000 genomes]
rs72623487	0.82[ASN][1000 genomes]
rs7320474	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326253	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7330356	0.82[CHB][hapmap]
rs7335148	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs765404	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981622	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7995666	0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9314975	0.82[ASN][1000 genomes]
rs9314978	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9506226	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9506229	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9506231	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9506233	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9508553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9508554	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9508557	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9508558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9508559	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9508560	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508561	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9508564	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9508568	0.88[ASN][1000 genomes]
rs9550494	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9551741	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9551744	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9551751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9551753	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9578136	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9578139	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30376600-30420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:30392000-30415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:30404400-30420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr13:30404600-30415800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:30404800-30415600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:30404800-30418200	Weak transcription	HSMM	muscle
7	chr13:30405200-30415800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:30405400-30419200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:30406000-30415000	Weak transcription	NHEK	skin
10	chr13:30406000-30419600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr13:30406200-30417800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:30407200-30415800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:30407400-30415800	Weak transcription	Gastric	stomach
14	chr13:30407400-30419200	Weak transcription	Fetal Intestine Small	intestine
15	chr13:30407400-30419400	Weak transcription	Brain Angular Gyrus	brain
16	chr13:30407400-30419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:30407400-30419800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:30407400-30420800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr13:30407600-30415800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:30407600-30418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:30407800-30418600	Weak transcription	Brain Substantia Nigra	brain
22	chr13:30408200-30415800	Weak transcription	Pancreas	Pancrea
23	chr13:30408200-30420800	Weak transcription	Right Atrium	heart
24	chr13:30408400-30415800	Weak transcription	Aorta	Aorta
25	chr13:30408400-30415800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr13:30409800-30421600	Weak transcription	Left Ventricle	heart
27	chr13:30410000-30415800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr13:30410000-30420000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr13:30410200-30415600	Weak transcription	GM12878-XiMat	blood
30	chr13:30410800-30415800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr13:30411000-30415800	Weak transcription	Thymus	Thymus
32	chr13:30411000-30420800	Weak transcription	Ovary	ovary
33	chr13:30411200-30415800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr13:30411200-30415800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr13:30411200-30418200	Weak transcription	Osteobl	bone
36	chr13:30411200-30418600	Weak transcription	Adipose Nuclei	Adipose
37	chr13:30411800-30415800	Weak transcription	Stomach Mucosa	stomach
38	chr13:30412000-30416000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:30412000-30416000	Weak transcription	Psoas Muscle	Psoas
40	chr13:30412000-30421000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:30412400-30415000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr13:30412600-30416200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:30413200-30415600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:30413200-30420600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr13:30413400-30415600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr13:30413400-30415600	Weak transcription	Primary T cells from cord blood	blood
47	chr13:30413800-30415000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:30413800-30420400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr13:30414000-30416600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr13:30414200-30415200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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