Variant report

Variant	rs2788605
Chromosome Location	chr1:9869921-9869922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9867142..9871724-chr1:9879944..9886157,6	K562	blood:
2	chr1:9869713..9873865-chr1:9879645..9884796,5	MCF-7	breast:
3	chr1:9867174..9870965-chr1:9881963..9885357,3	K562	blood:
4	chr1:9858725..9860856-chr1:9868974..9871058,2	K562	blood:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10779731	0.84[EUR][1000 genomes]
rs10864436	0.82[EUR][1000 genomes]
rs10864437	0.82[EUR][1000 genomes]
rs10864438	0.84[EUR][1000 genomes]
rs11121492	0.86[EUR][1000 genomes]
rs11121493	0.94[EUR][1000 genomes]
rs11674	0.84[EUR][1000 genomes]
rs11806520	0.87[EUR][1000 genomes]
rs12034239	0.91[EUR][1000 genomes]
rs12078414	0.87[EUR][1000 genomes]
rs12087051	0.91[EUR][1000 genomes]
rs12088273	0.82[EUR][1000 genomes]
rs1228434	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1615629	0.86[EUR][1000 genomes]
rs1631962	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1660741	0.86[EUR][1000 genomes]
rs1660742	0.86[EUR][1000 genomes]
rs17034335	0.86[EUR][1000 genomes]
rs17034340	0.86[EUR][1000 genomes]
rs1767271	0.81[ASN][1000 genomes]
rs1767277	0.87[EUR][1000 genomes]
rs41280776	0.89[ASN][1000 genomes]
rs4585981	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109009	0.84[EUR][1000 genomes]
rs57480158	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57560942	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59729812	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6699320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855716	0.84[EUR][1000 genomes]
rs72855733	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855745	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72855747	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7550246	0.84[EUR][1000 genomes]
rs767762	0.87[EUR][1000 genomes]
rs935071	0.91[EUR][1000 genomes]
rs946277	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946278	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946279	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9854000-9871600	Weak transcription	Brain Germinal Matrix	brain
2	chr1:9859000-9870800	Weak transcription	Fetal Brain Female	brain
3	chr1:9859000-9871400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:9859000-9875000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:9859000-9881800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:9859000-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:9859200-9871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:9859200-9871400	Weak transcription	A549	lung
9	chr1:9859200-9871800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:9859200-9874200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:9859200-9874800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:9859400-9881600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:9860400-9878600	Weak transcription	Primary B cells from cord blood	blood
14	chr1:9863400-9873200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:9865000-9874600	Weak transcription	Fetal Intestine Large	intestine
16	chr1:9865000-9874800	Weak transcription	Placenta	Placenta
17	chr1:9865000-9882200	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:9865400-9881600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:9865600-9871000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:9865600-9871200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:9865600-9871400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:9865600-9871400	Weak transcription	Stomach Mucosa	stomach
23	chr1:9865600-9873000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:9865600-9873600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:9865600-9877000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:9865600-9879000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:9865600-9880800	Weak transcription	Hela-S3	cervix
28	chr1:9865600-9882200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:9866400-9880600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:9866600-9871200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:9866600-9871400	Weak transcription	HepG2	liver
32	chr1:9866800-9870600	Enhancers	Pancreas	Pancrea
33	chr1:9867000-9870000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:9867200-9870000	Enhancers	Gastric	stomach
35	chr1:9868200-9870000	Enhancers	Fetal Heart	heart
36	chr1:9868200-9874800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:9868200-9874800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:9868200-9875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:9868200-9882600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:9868400-9870000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:9868400-9870000	Enhancers	Colon Smooth Muscle	Colon
42	chr1:9868400-9870600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:9868400-9880800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:9868400-9880800	Weak transcription	Primary T cells from cord blood	blood
45	chr1:9868400-9882600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:9868600-9870000	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr1:9868600-9870600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:9868800-9870000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:9868800-9870000	Enhancers	Right Ventricle	heart
50	chr1:9868800-9870200	Enhancers	HMEC	breast

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