Variant report

Variant	rs2761939
Chromosome Location	chr13:30408738-30408739
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30407821..30411668-chr13:30422825..30425033,3	MCF-7	breast:
2	chr13:30406067..30409440-chr13:30410135..30412697,3	K562	blood:
3	chr13:30408592..30412430-chr13:30415846..30421304,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11147398	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12872400	0.88[ASN][1000 genomes]
rs1323931	0.87[ASN][1000 genomes]
rs1410110	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1854176	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1927193	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2025604	0.86[ASN][1000 genomes]
rs2182129	0.86[ASN][1000 genomes]
rs2388246	0.86[ASN][1000 genomes]
rs2388247	0.83[ASN][1000 genomes]
rs2487664	0.85[AFR][1000 genomes]
rs2761938	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2761940	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278034	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35541102	0.88[ASN][1000 genomes]
rs4083610	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4238128	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265673	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4297554	0.87[ASN][1000 genomes]
rs4769772	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4769775	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6490429	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6490430	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7320474	0.87[ASN][1000 genomes]
rs7326253	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7330356	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7335148	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7342470	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs765404	0.86[ASN][1000 genomes]
rs7981622	0.86[ASN][1000 genomes]
rs7995666	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9314972	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9314973	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9314974	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9314978	0.87[ASN][1000 genomes]
rs9506226	0.86[ASN][1000 genomes]
rs9506229	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9506231	0.87[ASN][1000 genomes]
rs9506233	0.86[ASN][1000 genomes]
rs9508550	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9508553	0.84[ASN][1000 genomes]
rs9508554	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9508557	0.87[ASN][1000 genomes]
rs9508558	0.87[ASN][1000 genomes]
rs9508559	0.88[ASN][1000 genomes]
rs9508560	0.84[ASN][1000 genomes]
rs9508564	0.87[ASN][1000 genomes]
rs9508568	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9550494	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9551739	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9551744	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9551751	0.87[ASN][1000 genomes]
rs9551753	0.81[ASN][1000 genomes]
rs9578139	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:63 , 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	chr13:30385800-30410600	Weak transcription	Small Intestine	intestine
3	chr13:30391200-30410600	Weak transcription	Ovary	ovary
4	chr13:30392000-30415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:30394000-30410600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr13:30394200-30413400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr13:30394400-30410600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr13:30402000-30409400	Weak transcription	Primary B cells from cord blood	blood
9	chr13:30404400-30420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:30404600-30415800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:30404800-30415600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:30404800-30418200	Weak transcription	HSMM	muscle
13	chr13:30405000-30410600	Weak transcription	Osteobl	bone
14	chr13:30405200-30408800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:30405200-30409400	Weak transcription	Adipose Nuclei	Adipose
16	chr13:30405200-30409400	Weak transcription	Brain Anterior Caudate	brain
17	chr13:30405200-30410000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr13:30405200-30415800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr13:30405400-30410600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:30405400-30419200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:30405600-30414800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr13:30406000-30415000	Weak transcription	NHEK	skin
23	chr13:30406000-30419600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr13:30406200-30410600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr13:30406200-30417800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:30406800-30409800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:30407200-30409800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr13:30407200-30414200	Weak transcription	Hela-S3	cervix
29	chr13:30407200-30415800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:30407400-30409400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr13:30407400-30410200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr13:30407400-30410600	Weak transcription	Liver	Liver
33	chr13:30407400-30412200	Weak transcription	Primary T cells from cord blood	blood
34	chr13:30407400-30415800	Weak transcription	Gastric	stomach
35	chr13:30407400-30419200	Weak transcription	Fetal Intestine Small	intestine
36	chr13:30407400-30419400	Weak transcription	Brain Angular Gyrus	brain
37	chr13:30407400-30419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:30407400-30419800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:30407400-30420800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr13:30407600-30409400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr13:30407600-30411000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr13:30407600-30411600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr13:30407600-30415800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr13:30407600-30418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr13:30407800-30410200	Weak transcription	Stomach Mucosa	stomach
46	chr13:30407800-30410600	Weak transcription	Brain Hippocampus Middle	brain
47	chr13:30407800-30414200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr13:30407800-30418600	Weak transcription	Brain Substantia Nigra	brain
49	chr13:30408000-30410600	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:30408200-30409600	Weak transcription	H1 Cell Line	embryonic stem cell

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