Variant report

Variant	rs55785223
Chromosome Location	chr2:38775175-38775176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38741728..38744582-chr2:38773775..38776381,2	K562	blood:
2	chr2:38772538..38776626-chr2:38827465..38831623,3	K562	blood:
3	chr2:38773369..38778839-chr2:38780028..38785171,8	K562	blood:
4	chr2:38771801..38777092-chr2:38966712..38971904,5	K562	blood:
5	chr2:38767365..38769438-chr2:38773461..38775183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000231367	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12614876	1.00[EUR][1000 genomes]
rs12616367	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619629	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12621565	0.83[EUR][1000 genomes]
rs12621788	1.00[EUR][1000 genomes]
rs1543880	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1543881	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17022945	0.87[AMR][1000 genomes]
rs17576044	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17603782	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34133986	0.83[EUR][1000 genomes]
rs36024292	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3765001	0.83[EUR][1000 genomes]
rs41446253	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55833813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55957936	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56251362	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56956410	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58720388	0.83[EUR][1000 genomes]
rs59065420	0.83[EUR][1000 genomes]
rs59114683	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60475078	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6727765	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6732743	0.87[AMR][1000 genomes]
rs6754893	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72895897	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72897608	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72897610	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905831	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72905837	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72905843	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905844	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905847	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905860	0.82[AFR][1000 genomes]
rs72905861	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905863	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905868	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905869	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905871	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72905880	0.87[AMR][1000 genomes]
rs73929040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73929050	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73929052	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73929077	0.87[AMR][1000 genomes]
rs7579783	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584862	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606515	0.83[EUR][1000 genomes];0.89[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
4	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:38768800-38779000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:38769200-38776800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:38769200-38782800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:38769600-38775600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:38769600-38777000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:38770200-38777600	Weak transcription	HSMM	muscle
17	chr2:38770200-38781000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:38770400-38776200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:38770400-38776200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:38770400-38776400	Weak transcription	Ovary	ovary
21	chr2:38770400-38778400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:38770400-38778800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:38770400-38778800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:38770400-38778800	Weak transcription	HSMMtube	muscle
25	chr2:38770400-38786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:38770400-38787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:38770400-38787200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:38770400-38787200	Weak transcription	Fetal Intestine Large	intestine
29	chr2:38770400-38787200	Weak transcription	NHLF	lung
30	chr2:38770400-38787200	Weak transcription	Osteobl	bone
31	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:38770600-38776000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:38770600-38785800	Weak transcription	NH-A	brain
37	chr2:38770600-38787400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:38770600-38794800	Weak transcription	NHEK	skin
39	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:38771000-38776000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:38771000-38779400	Weak transcription	Fetal Thymus	thymus
42	chr2:38771000-38786200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:38771200-38776200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:38771200-38776200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:38771200-38776200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:38771200-38776400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:38771200-38778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:38771200-38781000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:38771200-38787200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:38771200-38787400	Weak transcription	HUVEC	blood vessel

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