Variant report

Variant	rs2647478
Chromosome Location	chr1:220212954-220212955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220212894..220215277-chr1:220216645..220218222,3	K562	blood:
2	chr1:220212014..220214068-chr1:220216759..220219974,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136628	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10442684	0.84[EUR][1000 genomes]
rs10746395	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10746396	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779395	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10779396	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12141971	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12142009	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1566252	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1611961	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1612144	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1614384	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1614585	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1614719	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1622508	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1658226	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1658227	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1694576	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1694599	0.81[EUR][1000 genomes]
rs1694600	0.81[EUR][1000 genomes]
rs1768665	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1768667	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1768669	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1768670	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1768671	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1768674	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1768676	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1768677	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2230301	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245457	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248466	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248479	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248717	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2248719	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2577138	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577139	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577140	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577141	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577142	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577144	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577145	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577146	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577147	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577148	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577149	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577150	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577151	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2577156	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2577158	0.85[EUR][1000 genomes]
rs2577159	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577160	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2577163	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2577165	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647420	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647421	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2647422	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647423	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647424	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647426	0.86[EUR][1000 genomes]
rs2647427	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2647428	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647429	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647430	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647431	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2647432	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2647433	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2647434	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2647438	0.81[EUR][1000 genomes]
rs2647445	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647446	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647447	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647448	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647449	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647451	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647452	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647454	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647455	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647456	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2647457	0.88[EUR][1000 genomes]
rs2647462	0.81[EUR][1000 genomes]
rs2647467	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2647469	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647470	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2647479	0.93[EUR][1000 genomes]
rs2789793	0.82[EUR][1000 genomes]
rs2789794	0.93[EUR][1000 genomes]
rs2789797	0.93[EUR][1000 genomes]
rs2789800	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789802	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789803	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2789806	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2789807	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789808	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2789809	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789810	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789811	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789812	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789813	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789815	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2789816	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789817	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789819	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795310	0.93[EUR][1000 genomes]
rs2795314	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41274790	0.94[ASN][1000 genomes]
rs6541120	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6681055	0.83[EUR][1000 genomes]
rs6681471	0.92[EUR][1000 genomes]
rs6681474	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703042	0.90[EUR][1000 genomes]
rs7537058	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7545314	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7548397	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7550249	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv3388149	chr1:220205606-220233828	Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220168400-220213800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:220170400-220218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:220172600-220218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:220178000-220217800	Weak transcription	Pancreas	Pancrea
5	chr1:220178200-220218600	Weak transcription	Right Ventricle	heart
6	chr1:220187200-220216800	Weak transcription	Fetal Heart	heart
7	chr1:220187400-220216800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:220193600-220218600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:220196400-220218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:220197200-220217800	Weak transcription	Colonic Mucosa	Colon
11	chr1:220199600-220216800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:220203400-220218600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:220205200-220216800	Weak transcription	Fetal Brain Male	brain
14	chr1:220205200-220218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:220206600-220217000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:220206800-220213000	Weak transcription	Psoas Muscle	Psoas
17	chr1:220206800-220218200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:220206800-220219000	Weak transcription	Fetal Lung	lung
19	chr1:220207600-220217000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:220207600-220218200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:220208000-220216400	Weak transcription	NHDF-Ad	bronchial
22	chr1:220208200-220216800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:220208200-220218200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:220208400-220218200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:220208600-220218000	Weak transcription	HSMM	muscle
26	chr1:220208800-220218400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:220209000-220214200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:220209400-220213600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:220209600-220215200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:220209800-220214000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:220210400-220213800	Strong transcription	Fetal Thymus	thymus
32	chr1:220210600-220218600	Weak transcription	Right Atrium	heart
33	chr1:220210800-220213800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:220210800-220213800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:220210800-220214200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:220211000-220213400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:220211000-220213800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:220211000-220213800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:220211000-220213800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:220211000-220214000	Strong transcription	Hela-S3	cervix
41	chr1:220211000-220214600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:220211000-220214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:220211000-220214800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:220211200-220213400	Strong transcription	Osteobl	bone
45	chr1:220211200-220213800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:220211200-220214000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:220211200-220214200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:220211200-220215400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:220211400-220214800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:220211600-220213200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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