Variant report

Variant	rs11887454
Chromosome Location	chr2:173434765-173434766
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr2:173434421-173434941	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:173434601-173434961	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173418979..173421868-chr2:173434562..173438051,3	K562	blood:

Variant related genes	Relation type
PDK1	TF binding region
ENSG00000225205	Chromatin interaction
ENSG00000152256	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10048692	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048707	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048825	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176813	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181851	0.81[EUR][1000 genomes]
rs10186869	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197678	0.93[ASN][1000 genomes]
rs10199472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207262	0.80[ASN][1000 genomes]
rs10208151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427189	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427315	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451559	0.88[CEU][hapmap]
rs1075638	0.81[EUR][1000 genomes]
rs10930562	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs10930565	0.84[EUR][1000 genomes]
rs11890159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891127	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895461	1.00[CHB][hapmap]
rs11896032	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896178	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897165	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897495	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897582	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898137	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11898890	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901110	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901586	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11902810	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902907	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904366	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693007	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990751	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008835	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009291	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010205	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012115	0.90[CEU][hapmap]
rs13021042	0.81[CEU][hapmap]
rs13023751	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024218	0.80[ASN][1000 genomes]
rs13024431	0.80[ASN][1000 genomes]
rs13032610	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032692	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385644	0.93[ASN][1000 genomes]
rs13386103	1.00[ASN][1000 genomes]
rs13388338	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398305	0.82[CEU][hapmap]
rs13401945	0.80[ASN][1000 genomes]
rs13401980	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405998	0.80[ASN][1000 genomes]
rs13408780	0.80[ASN][1000 genomes]
rs13415156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13415174	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425344	0.80[ASN][1000 genomes]
rs1531151	0.80[ASN][1000 genomes]
rs16860696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740327	0.82[CEU][hapmap]
rs1869922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982410	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290564	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599267	0.80[ASN][1000 genomes]
rs2606069	0.80[ASN][1000 genomes]
rs28537209	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087500	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139806	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611798	0.80[ASN][1000 genomes]
rs34707897	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34888332	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35086707	0.80[ASN][1000 genomes]
rs35156154	0.80[ASN][1000 genomes]
rs35665064	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35809888	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880823	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951155	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999155	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36118221	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3613	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765065	0.82[EUR][1000 genomes]
rs3769321	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs3792259	0.82[CEU][hapmap]
rs3816536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56953655	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59004833	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59104969	0.93[ASN][1000 genomes]
rs62167832	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62167835	0.84[EUR][1000 genomes]
rs62169270	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169301	0.80[ASN][1000 genomes]
rs66460331	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710129	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6723872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738196	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs6752257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752386	0.84[EUR][1000 genomes]
rs70937080	0.93[ASN][1000 genomes]
rs7566884	0.93[ASN][1000 genomes]
rs7567092	0.93[ASN][1000 genomes]
rs7596665	0.90[CEU][hapmap]
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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173421400-173436200	Weak transcription	Spleen	Spleen
2	chr2:173421600-173436000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:173421600-173436000	Weak transcription	Lung	lung
4	chr2:173421600-173453400	Weak transcription	Pancreas	Pancrea
5	chr2:173421800-173439000	Weak transcription	Psoas Muscle	Psoas
6	chr2:173421800-173443600	Weak transcription	Ovary	ovary
7	chr2:173421800-173465200	Weak transcription	Small Intestine	intestine
8	chr2:173422000-173437600	Weak transcription	A549	lung
9	chr2:173422000-173438600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:173422000-173439000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:173422000-173443600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:173422200-173436200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:173422200-173437000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:173422200-173437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:173422200-173438600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:173422200-173451000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:173422600-173438800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:173423400-173438600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr2:173423400-173441400	Weak transcription	Fetal Kidney	kidney
20	chr2:173423400-173451000	Weak transcription	Colonic Mucosa	Colon
21	chr2:173423600-173436800	Strong transcription	Dnd41	blood
22	chr2:173423600-173438600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:173423600-173439600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:173423600-173443600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:173424400-173439400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:173424600-173440200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:173424600-173447800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:173425000-173438600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:173425000-173438800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:173426200-173439200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:173426200-173460600	Weak transcription	HSMMtube	muscle
32	chr2:173426400-173438600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:173426400-173438600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:173426400-173438600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:173426400-173438800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:173426400-173439000	Weak transcription	Brain Germinal Matrix	brain
37	chr2:173426800-173439000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr2:173426800-173439000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:173426800-173439400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:173426800-173443600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:173427000-173437600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:173427000-173438000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:173427000-173438000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:173427000-173438200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:173427000-173438400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:173427000-173438600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:173427000-173439200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:173427200-173439000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:173427200-173439600	Strong transcription	Liver	Liver
50	chr2:173427400-173435400	Weak transcription	Left Ventricle	heart

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