Variant report

Variant	rs4641990
Chromosome Location	chr2:48560987-48560988
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48540779..48543289-chr2:48560112..48562451,2	K562	blood:
2	chr2:48559983..48562796-chr2:48566723..48568963,3	K562	blood:
3	chr2:48558442..48561276-chr2:48561458..48563692,2	K562	blood:
4	chr2:48559522..48562446-chr2:48563870..48566960,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251889	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10153773	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10174717	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10180295	0.88[ASN][1000 genomes]
rs10186237	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10193072	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10199431	1.00[CHB][hapmap];0.96[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10208124	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10495951	0.91[JPT][hapmap]
rs10495952	0.91[JPT][hapmap]
rs11676168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11679523	0.91[JPT][hapmap]
rs11680916	0.95[JPT][hapmap]
rs11682044	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs11685861	0.91[JPT][hapmap];0.88[YRI][hapmap]
rs11688481	0.91[JPT][hapmap]
rs11690690	0.91[JPT][hapmap];0.85[YRI][hapmap]
rs11690748	0.91[JPT][hapmap]
rs11690845	0.91[JPT][hapmap]
rs13383364	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13385535	0.95[ASN][1000 genomes]
rs13386751	0.83[ASN][1000 genomes]
rs13387171	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13388291	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13426834	0.83[ASN][1000 genomes]
rs13432998	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17037289	0.91[JPT][hapmap]
rs17037298	0.91[JPT][hapmap]
rs17855177	0.91[JPT][hapmap]
rs28806843	0.88[ASN][1000 genomes]
rs28841370	0.91[ASN][1000 genomes]
rs4290706	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4344965	0.91[JPT][hapmap]
rs4411759	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4438532	0.84[CEU][hapmap]
rs4547573	1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs4606978	0.84[CEU][hapmap]
rs56352447	0.96[ASN][1000 genomes]
rs57668696	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs58660534	0.93[ASN][1000 genomes]
rs59264464	0.91[ASN][1000 genomes]
rs59412192	0.91[ASN][1000 genomes]
rs59761994	0.93[ASN][1000 genomes]
rs60677957	0.84[ASN][1000 genomes]
rs62136987	0.92[ASN][1000 genomes]
rs62137001	0.93[ASN][1000 genomes]
rs62137002	0.93[ASN][1000 genomes]
rs62137003	0.93[ASN][1000 genomes]
rs62137005	0.93[ASN][1000 genomes]
rs62137006	0.91[ASN][1000 genomes]
rs62137007	0.91[ASN][1000 genomes]
rs62137008	0.89[ASN][1000 genomes]
rs62137009	0.89[ASN][1000 genomes]
rs62138801	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6545027	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6545028	0.85[ASN][1000 genomes]
rs6545029	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6545030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6545034	0.90[ASN][1000 genomes]
rs6545035	0.90[ASN][1000 genomes]
rs6545036	0.84[YRI][hapmap]
rs6705802	0.91[JPT][hapmap]
rs6712029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6718068	0.91[JPT][hapmap]
rs6743757	0.91[JPT][hapmap]
rs6757206	0.89[ASN][1000 genomes]
rs72818493	0.90[ASN][1000 genomes]
rs72820405	0.93[ASN][1000 genomes]
rs72887649	0.90[ASN][1000 genomes]
rs7562069	0.91[JPT][hapmap]
rs7562816	0.91[JPT][hapmap]
rs7566239	0.91[JPT][hapmap];0.82[YRI][hapmap]
rs7568960	0.82[ASN][1000 genomes]
rs7574125	0.84[ASN][1000 genomes]
rs7576964	0.86[JPT][hapmap];0.80[YRI][hapmap]
rs7577237	0.91[JPT][hapmap];0.84[YRI][hapmap]
rs7579932	0.91[JPT][hapmap];0.82[YRI][hapmap]
rs7600794	0.91[JPT][hapmap];0.85[YRI][hapmap]
rs7606104	0.91[JPT][hapmap];0.88[YRI][hapmap]
rs9309152	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4641990	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543400-48568600	Weak transcription	HSMM	muscle
2	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:48544400-48570400	Weak transcription	NHEK	skin
5	chr2:48544400-48570800	Weak transcription	HMEC	breast
6	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:48550400-48562200	Enhancers	Brain Substantia Nigra	brain
9	chr2:48552400-48561000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:48552400-48561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:48552400-48566200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:48552400-48570600	Weak transcription	Aorta	Aorta
13	chr2:48553400-48574400	Weak transcription	Lung	lung
14	chr2:48553800-48570800	Weak transcription	Thymus	Thymus
15	chr2:48554400-48561000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr2:48554400-48570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:48554800-48561600	Weak transcription	Psoas Muscle	Psoas
18	chr2:48554800-48562000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:48555000-48561600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:48555000-48562000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:48555400-48570600	Weak transcription	NHLF	lung
22	chr2:48556800-48562800	Enhancers	Brain Angular Gyrus	brain
23	chr2:48556800-48570600	Weak transcription	Fetal Thymus	thymus
24	chr2:48556800-48571600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:48557000-48566600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:48557000-48567600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:48557200-48564400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:48557200-48568600	Weak transcription	HUVEC	blood vessel
31	chr2:48557800-48561400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:48557800-48570400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:48558000-48561200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:48558200-48568200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:48558400-48571400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:48558800-48561200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:48558800-48561400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:48558800-48566600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:48558800-48567400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:48558800-48568400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:48558800-48571200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:48559000-48561400	Weak transcription	K562	blood
43	chr2:48559000-48561600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:48559000-48561600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:48559000-48564400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:48559000-48570600	Weak transcription	Left Ventricle	heart
47	chr2:48559000-48570600	Weak transcription	Spleen	Spleen
48	chr2:48559400-48561600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr2:48559800-48561200	Weak transcription	Brain Anterior Caudate	brain
50	chr2:48559800-48561800	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links