Variant report

Variant	rs4893961
Chromosome Location	chr2:178411075-178411076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178409008..178411767-chr2:178429982..178431742,2	K562	blood:
2	chr2:178410398..178415306-chr2:178416256..178419727,5	K562	blood:

Variant related genes	Relation type
ENSG00000196659	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10165785	0.84[ASN][1000 genomes]
rs10170546	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs10170667	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10194648	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10201153	0.95[JPT][hapmap]
rs10497500	0.86[JPT][hapmap]
rs10497501	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10497502	0.85[JPT][hapmap]
rs10497503	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497508	0.85[JPT][hapmap]
rs10803909	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930792	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930798	0.81[EUR][1000 genomes]
rs11684320	0.81[EUR][1000 genomes]
rs11893448	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12104588	0.81[EUR][1000 genomes]
rs12463893	0.81[EUR][1000 genomes]
rs12469386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12471741	0.81[EUR][1000 genomes]
rs12612857	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs12615367	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12616093	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12616443	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618139	0.90[JPT][hapmap]
rs12622298	0.81[EUR][1000 genomes]
rs12693120	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12990729	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12996447	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13000048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004955	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13013752	0.81[EUR][1000 genomes]
rs13027959	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1348848	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1348849	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1348850	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1374437	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1405713	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1453370	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1453373	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1548067	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs16865203	0.85[JPT][hapmap]
rs16865291	0.86[JPT][hapmap]
rs16865328	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16865331	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1901825	0.90[JPT][hapmap]
rs1901826	0.85[JPT][hapmap]
rs1975543	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979058	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2034678	0.86[JPT][hapmap]
rs2060929	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2084233	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2121430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2166558	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2197611	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213945	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3769995	0.86[JPT][hapmap]
rs3769996	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3769997	0.86[JPT][hapmap]
rs3770002	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3813259	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs3902850	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3927978	0.82[EUR][1000 genomes]
rs4243388	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4243390	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4341974	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4528793	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs4893821	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4893822	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4893823	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4893824	0.84[ASN][1000 genomes]
rs4893825	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4893935	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4893936	0.91[JPT][hapmap]
rs4893938	0.81[EUR][1000 genomes]
rs4893941	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4893944	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893945	0.83[ASN][1000 genomes]
rs4893946	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4893950	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4893954	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893957	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893959	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893962	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4893965	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6433670	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433673	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710575	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6742951	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6761593	0.83[EUR][1000 genomes]
rs7565022	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586051	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7587604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7591807	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs7604673	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606235	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7607450	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8941	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs952746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9679607	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9789582	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4893961	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178358600-178417000	Weak transcription	Aorta	Aorta
2	chr2:178364400-178416600	Weak transcription	Esophagus	oesophagus
3	chr2:178372800-178416600	Weak transcription	A549	lung
4	chr2:178375600-178413800	Weak transcription	K562	blood
5	chr2:178376200-178416600	Weak transcription	Pancreas	Pancrea
6	chr2:178388600-178416600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:178389000-178416800	Weak transcription	Small Intestine	intestine
8	chr2:178389200-178416600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:178389800-178416800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:178390600-178416600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:178391000-178413400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:178392000-178416800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:178401000-178416600	Weak transcription	Lung	lung
14	chr2:178402800-178416600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:178403600-178411200	Weak transcription	Primary T cells from cord blood	blood
16	chr2:178403600-178416600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:178403800-178416600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:178403800-178416800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:178404000-178412000	Weak transcription	HUVEC	blood vessel
20	chr2:178405400-178416600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:178405400-178416800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:178406200-178416600	Weak transcription	HepG2	liver
23	chr2:178407800-178416800	Weak transcription	Fetal Brain Male	brain
24	chr2:178408000-178411600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:178408800-178416600	Weak transcription	HSMM	muscle
26	chr2:178409000-178411400	Enhancers	GM12878-XiMat	blood
27	chr2:178409000-178413000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:178409200-178412600	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:178409400-178411400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:178409400-178416400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:178409400-178416400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:178409600-178416600	Weak transcription	Osteobl	bone
33	chr2:178410000-178411600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:178410200-178411600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr2:178410600-178411400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:178410600-178411400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr2:178410600-178412000	Enhancers	Adipose Nuclei	Adipose

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