Variant report

Variant	rs2440909
Chromosome Location	chr10:61639377-61639378
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:61633082..61635671-chr10:61637536..61639687,3	MCF-7	breast:
2	chr10:61638398..61641573-chr10:61642787..61646612,4	K562	blood:
3	chr10:61636740..61643413-chr10:61643807..61649213,6	K562	blood:
4	chr10:61639063..61643015-chr10:61647185..61650219,3	MCF-7	breast:
5	chr10:61628363..61632189-chr10:61637394..61643761,6	K562	blood:
6	chr10:61634142..61636332-chr10:61636728..61639636,2	MCF-7	breast:
7	chr10:61638896..61642309-chr10:61665188..61667493,3	K562	blood:
8	chr10:61633677..61637740-chr10:61638115..61642166,4	K562	blood:
9	chr10:61635533..61637804-chr10:61638300..61641205,3	K562	blood:
10	chr10:61594890..61595766-chr10:61639203..61639741,2	MCF-7	breast:
11	chr10:61639233..61641192-chr10:61644964..61647007,2	MCF-7	breast:
12	chr10:61615566..61617712-chr10:61637129..61639962,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1171787	0.95[ASN][1000 genomes]
rs1624715	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627130	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627152	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628136	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664254	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664257	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664258	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664260	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664261	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664262	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664263	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684898	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684900	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684902	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684903	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17202345	0.80[EUR][1000 genomes]
rs2440906	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440908	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440910	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440911	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450468	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450469	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2450471	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146652	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895243	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795420	chr10:61637271-61669227	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:61630000-61647800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:61633000-61640600	Weak transcription	Gastric	stomach
6	chr10:61633200-61639400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr10:61633200-61640600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:61633200-61641800	Weak transcription	Lung	lung
9	chr10:61633400-61639400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:61633400-61643200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:61633400-61645200	Weak transcription	Fetal Thymus	thymus
12	chr10:61633400-61647800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:61633400-61647800	Weak transcription	Fetal Muscle Leg	muscle
14	chr10:61633400-61647800	Weak transcription	Fetal Stomach	stomach
15	chr10:61633400-61648600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:61633600-61645200	Weak transcription	Brain Germinal Matrix	brain
17	chr10:61634000-61640400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr10:61634000-61645000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr10:61634000-61645600	Weak transcription	Fetal Lung	lung
20	chr10:61634000-61646800	Weak transcription	Adipose Nuclei	Adipose
21	chr10:61634400-61640200	Enhancers	Colon Smooth Muscle	Colon
22	chr10:61634400-61648800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:61634400-61649000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:61634400-61651200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr10:61634600-61640600	Weak transcription	Left Ventricle	heart
26	chr10:61634800-61640600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:61634800-61645200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:61635000-61644000	Weak transcription	Brain Angular Gyrus	brain
29	chr10:61635000-61645400	Weak transcription	Brain Substantia Nigra	brain
30	chr10:61635000-61646800	Weak transcription	Right Ventricle	heart
31	chr10:61635400-61640800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr10:61635600-61639600	Weak transcription	HepG2	liver
33	chr10:61635600-61640600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr10:61635600-61640600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr10:61635600-61640800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr10:61635600-61640800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr10:61635600-61647600	Weak transcription	Brain Anterior Caudate	brain
38	chr10:61635800-61640800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr10:61635800-61641000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr10:61635800-61648600	Enhancers	Primary B cells from peripheral blood	blood
41	chr10:61636200-61641800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr10:61636600-61639800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr10:61636600-61641800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr10:61636800-61640600	Weak transcription	Fetal Intestine Small	intestine
45	chr10:61637000-61642200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:61637400-61641800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr10:61637400-61641800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr10:61637400-61645400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:61637400-61647800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:61637400-61648400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links