Variant report

Variant	rs9678904
Chromosome Location	chr2:48555585-48555586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48542620..48544627-chr2:48553697..48556453,2	K562	blood:
2	chr2:48549627..48551864-chr2:48552790..48555987,3	K562	blood:
3	chr2:48551728..48554180-chr2:48555389..48557801,2	MCF-7	breast:
4	chr2:48552083..48554152-chr2:48555088..48558115,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17037226	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17039245	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56806229	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59044598	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61405465	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6545032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6707607	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6709977	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6711828	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6723068	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6728719	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6731708	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6751375	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6757806	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72883965	1.00[AMR][1000 genomes]
rs72883976	1.00[AMR][1000 genomes]
rs72883981	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72885740	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72885747	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72885750	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72885760	1.00[AMR][1000 genomes]
rs72885796	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72885800	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72885801	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72889604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72889610	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7606543	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543400-48568600	Weak transcription	HSMM	muscle
2	chr2:48543600-48556600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:48543600-48559400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:48544200-48559600	Weak transcription	Fetal Kidney	kidney
7	chr2:48544400-48556200	Weak transcription	NHDF-Ad	bronchial
8	chr2:48544400-48558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:48544400-48570400	Weak transcription	NHEK	skin
10	chr2:48544400-48570800	Weak transcription	HMEC	breast
11	chr2:48544600-48558600	Weak transcription	Spleen	Spleen
12	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
13	chr2:48544800-48559400	Weak transcription	Right Atrium	heart
14	chr2:48546600-48556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:48548400-48556600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:48550400-48562200	Enhancers	Brain Substantia Nigra	brain
18	chr2:48550600-48559400	Enhancers	Brain Hippocampus Middle	brain
19	chr2:48551600-48558600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:48552000-48556600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:48552000-48556600	Weak transcription	HUVEC	blood vessel
22	chr2:48552000-48558800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr2:48552400-48556600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:48552400-48556600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:48552400-48556600	Weak transcription	Fetal Brain Male	brain
26	chr2:48552400-48557800	Weak transcription	K562	blood
27	chr2:48552400-48561000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:48552400-48561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:48552400-48566200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:48552400-48570600	Weak transcription	Aorta	Aorta
31	chr2:48552600-48555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:48552600-48556200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:48552600-48556600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:48553200-48555600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:48553200-48556200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:48553400-48558600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:48553400-48574400	Weak transcription	Lung	lung
38	chr2:48553600-48555600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:48553800-48555800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:48553800-48556200	Weak transcription	Brain Angular Gyrus	brain
41	chr2:48553800-48556600	Weak transcription	Small Intestine	intestine
42	chr2:48553800-48570800	Weak transcription	Thymus	Thymus
43	chr2:48554200-48555800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:48554400-48558200	Enhancers	A549	lung
45	chr2:48554400-48561000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr2:48554400-48570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:48554600-48555800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr2:48554800-48561600	Weak transcription	Psoas Muscle	Psoas
49	chr2:48554800-48562000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:48555000-48555800	Enhancers	Dnd41	blood

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