Variant report

Variant	rs7630869
Chromosome Location	chr3:49522543-49522544
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	chr3:49521377..49523560-chr3:49535457..49537721,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10212296	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1050088	0.82[ASN][1000 genomes]
rs10640	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130199	0.82[ASN][1000 genomes]
rs11130202	0.82[ASN][1000 genomes]
rs11130203	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706370	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11708955	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11711485	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712569	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713474	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11715915	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11716974	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11719996	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11720264	0.82[ASN][1000 genomes]
rs11720597	0.85[EUR][1000 genomes]
rs11922013	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11926781	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12330269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12489092	0.82[ASN][1000 genomes]
rs13062429	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13064576	0.83[EUR][1000 genomes]
rs13079082	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13079643	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13087851	0.81[AMR][1000 genomes]
rs1568661	0.82[ASN][1000 genomes]
rs1800668	0.81[AMR][1000 genomes]
rs1801143	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1987628	0.81[AMR][1000 genomes]
rs2312461	0.82[ASN][1000 genomes]
rs34196454	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34293138	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34363169	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34427167	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35115732	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35261698	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35701831	0.82[ASN][1000 genomes]
rs35999162	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3811697	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3870337	0.82[ASN][1000 genomes]
rs3870338	0.82[ASN][1000 genomes]
rs3877784	0.82[ASN][1000 genomes]
rs3924462	0.82[ASN][1000 genomes]
rs3926569	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4625	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855836	0.82[ASN][1000 genomes]
rs4855859	0.82[ASN][1000 genomes]
rs4855861	0.82[ASN][1000 genomes]
rs4855864	0.82[ASN][1000 genomes]
rs6446264	0.81[AMR][1000 genomes]
rs6446272	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446277	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67216675	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67485053	0.81[AMR][1000 genomes]
rs6766131	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6766581	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779524	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6797664	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6997	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71324962	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71615484	0.84[ASN][1000 genomes]
rs7622302	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633271	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7637999	0.82[ASN][1000 genomes]
rs7643845	0.82[ASN][1000 genomes]
rs7646366	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7648841	0.81[AMR][1000 genomes]
rs9814873	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9818590	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9821311	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9827021	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9837027	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9841110	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9850072	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9853683	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9858280	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9858418	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9859556	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9871380	0.82[AMR][1000 genomes]
rs9875617	0.86[EUR][1000 genomes]
rs9878943	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7630869	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs7630869	FAM212A	cis	Muscle Skeletal	GTEx
rs7630869	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49522800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49509800-49522800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:49509800-49522800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:49509800-49522800	Weak transcription	NHEK	skin
7	chr3:49509800-49523000	Weak transcription	Brain Substantia Nigra	brain
8	chr3:49509800-49531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:49510000-49522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:49510000-49523200	Weak transcription	Fetal Kidney	kidney
13	chr3:49510000-49526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:49510000-49535600	Weak transcription	NHLF	lung
15	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49511400-49522800	Weak transcription	Stomach Mucosa	stomach
17	chr3:49514400-49522800	Weak transcription	Osteobl	bone
18	chr3:49514400-49532400	Weak transcription	GM12878-XiMat	blood
19	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:49514800-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:49515000-49532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:49515200-49522800	Weak transcription	Adipose Nuclei	Adipose
24	chr3:49515200-49523000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:49515200-49524600	Weak transcription	Dnd41	blood
26	chr3:49515200-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:49515200-49532400	Weak transcription	Colonic Mucosa	Colon
28	chr3:49515400-49531000	Weak transcription	Gastric	stomach
29	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
31	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
32	chr3:49515600-49523000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:49515600-49523000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:49516600-49526600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:49516800-49522600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:49516800-49522800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:49516800-49525600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:49516800-49532400	Weak transcription	Small Intestine	intestine
39	chr3:49516800-49534800	Weak transcription	Liver	Liver
40	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:49517000-49522800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:49517000-49522800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:49517000-49522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:49517000-49522800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:49517000-49522800	Weak transcription	A549	lung
46	chr3:49517000-49525400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:49517200-49524800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:49517400-49530600	Weak transcription	Thymus	Thymus

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