Variant report

Variant	rs12990751
Chromosome Location	chr2:173440330-173440331
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173418730..173421118-chr2:173440176..173442867,3	K562	blood:

Variant related genes	Relation type
ENSG00000152256	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10048692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048825	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176813	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178654	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180021	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181851	0.80[EUR][1000 genomes]
rs10186869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197678	0.93[ASN][1000 genomes]
rs10199472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201129	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202550	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207262	0.80[ASN][1000 genomes]
rs10208151	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210546	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427189	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427315	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930562	0.83[EUR][1000 genomes]
rs10930565	0.83[EUR][1000 genomes]
rs11887454	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890159	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891127	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896032	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896178	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897495	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897582	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898137	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898890	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901110	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901586	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11902810	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902907	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904366	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693005	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007707	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008835	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009291	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010205	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023751	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024218	0.80[ASN][1000 genomes]
rs13024431	0.80[ASN][1000 genomes]
rs13032610	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032692	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385403	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385644	0.93[ASN][1000 genomes]
rs13386103	1.00[ASN][1000 genomes]
rs13388338	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394924	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401945	0.80[ASN][1000 genomes]
rs13401980	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405998	0.80[ASN][1000 genomes]
rs13408780	0.80[ASN][1000 genomes]
rs13415156	0.80[ASN][1000 genomes]
rs13415174	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417334	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425344	0.80[ASN][1000 genomes]
rs1531151	0.80[ASN][1000 genomes]
rs16860696	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860697	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299956	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702263	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869922	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982410	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290564	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599267	0.80[ASN][1000 genomes]
rs2606069	0.80[ASN][1000 genomes]
rs28537209	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087500	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611798	0.80[ASN][1000 genomes]
rs34707897	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34888332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35086707	0.80[ASN][1000 genomes]
rs35156154	0.80[ASN][1000 genomes]
rs35665064	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35809888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880823	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951155	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999155	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36118221	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3613	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765065	0.81[EUR][1000 genomes]
rs3769321	0.83[EUR][1000 genomes]
rs56953655	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59004833	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59104969	0.93[ASN][1000 genomes]
rs62167832	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62167835	0.83[EUR][1000 genomes]
rs62169270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169301	0.80[ASN][1000 genomes]
rs66460331	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710129	0.83[EUR][1000 genomes]
rs6723872	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738196	0.83[EUR][1000 genomes]
rs6752257	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752386	0.83[EUR][1000 genomes]
rs70937080	0.93[ASN][1000 genomes]
rs7566884	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7567092	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs836589	0.80[ASN][1000 genomes]
rs9287957	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv3035	chr2:173419058-173463901	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173421600-173453400	Weak transcription	Pancreas	Pancrea
2	chr2:173421800-173443600	Weak transcription	Ovary	ovary
3	chr2:173421800-173465200	Weak transcription	Small Intestine	intestine
4	chr2:173422000-173443600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:173422200-173451000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:173423400-173441400	Weak transcription	Fetal Kidney	kidney
7	chr2:173423400-173451000	Weak transcription	Colonic Mucosa	Colon
8	chr2:173423600-173443600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:173424600-173447800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:173426200-173460600	Weak transcription	HSMMtube	muscle
11	chr2:173426800-173443600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:173427400-173440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:173429400-173441600	Weak transcription	Fetal Heart	heart
14	chr2:173430600-173461600	Weak transcription	Right Ventricle	heart
15	chr2:173431400-173443600	Weak transcription	Aorta	Aorta
16	chr2:173431400-173480600	Weak transcription	Gastric	stomach
17	chr2:173432000-173462400	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:173433200-173440600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:173435000-173441400	Weak transcription	HSMM	muscle
20	chr2:173435600-173441600	Weak transcription	Hela-S3	cervix
21	chr2:173436000-173441000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:173436000-173445600	ZNF genes & repeats	GM12878-XiMat	blood
23	chr2:173436800-173443600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:173436800-173443600	Weak transcription	Esophagus	oesophagus
25	chr2:173436800-173444000	ZNF genes & repeats	Dnd41	blood
26	chr2:173437000-173451000	Weak transcription	Thymus	Thymus
27	chr2:173437000-173451800	Weak transcription	Spleen	Spleen
28	chr2:173437400-173449600	Weak transcription	Left Ventricle	heart
29	chr2:173437400-173452000	Weak transcription	Lung	lung
30	chr2:173437600-173441400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:173437600-173441600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:173437600-173443400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr2:173437600-173443800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:173437600-173449800	Weak transcription	Fetal Stomach	stomach
35	chr2:173437800-173442600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:173437800-173447000	Weak transcription	Placenta	Placenta
37	chr2:173438000-173445800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:173438200-173443400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:173438400-173440400	ZNF genes & repeats	Fetal Intestine Large	intestine
40	chr2:173438600-173440400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:173438600-173440600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:173438600-173441200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:173438600-173443200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
44	chr2:173438600-173445600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr2:173438800-173441800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr2:173438800-173442200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
47	chr2:173438800-173443800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:173439200-173440400	ZNF genes & repeats	NHEK	skin
49	chr2:173439200-173440600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:173439200-173442600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links