Variant report

Variant	rs62449639
Chromosome Location	chr7:27789526-27789527
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27787733..27790023-chr7:27790214..27791778,2	MCF-7	breast:
2	chr7:27784566..27786951-chr7:27787434..27790221,3	K562	blood:
3	chr7:27786993..27792954-chr7:27793164..27797918,6	K562	blood:
4	chr7:27701253..27703546-chr7:27787214..27789983,2	K562	blood:
5	chr7:27788924..27791824-chr7:27799682..27802351,2	K562	blood:

Variant related genes	Relation type
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10155851	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10225487	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10267854	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10277437	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10486559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951184	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12666082	0.85[EUR][1000 genomes]
rs16874364	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17150563	0.86[EUR][1000 genomes]
rs17155702	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17155943	0.81[EUR][1000 genomes]
rs2051830	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074579	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2074769	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107413	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2108309	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2158388	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237339	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237340	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237341	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237342	0.91[AFR][1000 genomes]
rs2285931	0.85[EUR][1000 genomes]
rs2299106	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2391488	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3779473	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4719907	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4719908	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4722741	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57932688	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58314651	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58857361	0.82[EUR][1000 genomes]
rs62449629	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62449640	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62451077	0.81[EUR][1000 genomes]
rs62451079	0.80[EUR][1000 genomes]
rs62454806	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62454945	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6462048	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6462049	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6462052	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6462053	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6944251	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6944913	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6971813	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6972821	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72598505	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7784038	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7801301	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7803019	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7803227	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7809735	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27780800-27796400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:27780800-27805600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:27780800-27810200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:27780800-27815200	Weak transcription	Gastric	stomach
5	chr7:27781000-27800200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
7	chr7:27781200-27789600	Weak transcription	Fetal Brain Female	brain
8	chr7:27781200-27790200	Weak transcription	Fetal Brain Male	brain
9	chr7:27781200-27791800	Weak transcription	Right Ventricle	heart
10	chr7:27781200-27792000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:27781400-27789600	Weak transcription	Esophagus	oesophagus
12	chr7:27781400-27799600	Weak transcription	Fetal Stomach	stomach
13	chr7:27781400-27803200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:27781400-27812800	Weak transcription	Brain Germinal Matrix	brain
15	chr7:27784800-27790400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:27784800-27799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:27784800-27801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:27784800-27834000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:27785000-27789800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:27785000-27789800	Weak transcription	Brain Angular Gyrus	brain
22	chr7:27785000-27793200	Weak transcription	Fetal Heart	heart
23	chr7:27785000-27805600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:27785000-27806200	Weak transcription	Spleen	Spleen
25	chr7:27785000-27825000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:27785200-27789800	Weak transcription	Fetal Lung	lung
27	chr7:27785200-27789800	Weak transcription	Hela-S3	cervix
28	chr7:27785200-27791000	Weak transcription	Fetal Kidney	kidney
29	chr7:27785200-27809800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:27786800-27789600	Weak transcription	NHLF	lung
31	chr7:27787000-27804200	Weak transcription	Fetal Intestine Small	intestine
32	chr7:27787400-27799200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:27787600-27793600	Weak transcription	Stomach Mucosa	stomach
34	chr7:27787600-27805600	Weak transcription	Pancreas	Pancrea
35	chr7:27787600-27825000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:27787800-27789600	Weak transcription	Psoas Muscle	Psoas
37	chr7:27787800-27789800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:27787800-27790400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:27787800-27791600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:27787800-27793400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:27787800-27793800	Strong transcription	Primary B cells from cord blood	blood
42	chr7:27787800-27826600	Weak transcription	Small Intestine	intestine
43	chr7:27788000-27789600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:27788000-27791000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:27788000-27791400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:27788000-27791800	Strong transcription	NHDF-Ad	bronchial
47	chr7:27788000-27792600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:27788000-27792600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:27788000-27792800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:27788000-27792800	Strong transcription	Monocytes-CD14+_RO01746	blood

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