Variant report

Variant	rs9827021
Chromosome Location	chr3:49514764-49514765
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	chr3:49506042..49510740-chr3:49512000..49516237,8	MCF-7	breast:
2	chr3:49507938..49509712-chr3:49512685..49515016,2	K562	blood:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10212296	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1050088	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1050450	0.85[AMR][1000 genomes]
rs10640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10865955	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11130192	1.00[JPT][hapmap]
rs11130199	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130202	0.94[ASN][1000 genomes]
rs11130203	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130206	0.84[ASN][1000 genomes]
rs11130213	1.00[CEU][hapmap]
rs1131095	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11706370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11708955	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11711485	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711536	0.82[AMR][1000 genomes]
rs11712569	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713474	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11716974	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11718165	1.00[CEU][hapmap]
rs11719996	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720264	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11720458	0.86[ASN][1000 genomes]
rs11720597	0.86[EUR][1000 genomes]
rs11919311	0.86[JPT][hapmap]
rs11922013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11926781	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12330269	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488065	0.88[ASN][1000 genomes]
rs12489092	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13062429	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13064576	0.84[EUR][1000 genomes]
rs13079082	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079643	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13087851	0.83[AMR][1000 genomes]
rs13090388	0.85[AMR][1000 genomes]
rs1464566	1.00[JPT][hapmap]
rs1464567	1.00[JPT][hapmap]
rs1464568	1.00[JPT][hapmap]
rs1568661	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17080528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17650792	1.00[JPT][hapmap]
rs1800668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs1801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873625	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1873626	0.88[JPT][hapmap]
rs1987628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2172252	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2312461	0.94[ASN][1000 genomes]
rs2329020	0.86[JPT][hapmap]
rs34196454	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34293138	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34363169	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427167	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34588335	0.85[AMR][1000 genomes]
rs34762726	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs35115732	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35169793	0.85[AMR][1000 genomes]
rs35261698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35701831	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35999162	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811697	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs3870337	0.94[ASN][1000 genomes]
rs3870338	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3877784	0.94[ASN][1000 genomes]
rs3924462	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3926569	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241406	0.86[ASN][1000 genomes]
rs4283605	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855836	0.94[ASN][1000 genomes]
rs4855839	1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap]
rs4855852	0.86[JPT][hapmap]
rs4855855	0.85[ASN][1000 genomes]
rs4855859	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855861	0.94[ASN][1000 genomes]
rs4855864	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855866	0.80[ASN][1000 genomes]
rs4855873	1.00[JPT][hapmap]
rs4855877	1.00[JPT][hapmap]
rs56116382	0.87[ASN][1000 genomes]
rs62261185	0.81[ASN][1000 genomes]
rs6446264	0.83[AMR][1000 genomes]
rs6446272	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6446277	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67216675	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67485053	0.83[AMR][1000 genomes]
rs6766131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766581	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770670	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs6779524	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6782577	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6784820	1.00[JPT][hapmap]
rs6793308	0.85[AMR][1000 genomes]
rs6797664	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803222	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6809216	0.85[AMR][1000 genomes]
rs6997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71324962	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71615484	0.96[ASN][1000 genomes]
rs7371895	0.82[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623659	0.85[AMR][1000 genomes]
rs7630869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637999	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7643845	0.94[ASN][1000 genomes]
rs7646366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7648841	0.83[AMR][1000 genomes]
rs885592	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9814873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9818590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap]
rs9827708	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9837027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837341	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850072	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858418	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9858542	1.00[CEU][hapmap]
rs9859556	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9871380	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9875617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs9878943	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9882740	1.00[CEU][hapmap];0.86[JPT][hapmap]

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
rs9827021	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9827021	FAM212A	cis	Muscle Skeletal	GTEx
rs9827021	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509400-49520200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:49509600-49514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:49509600-49519000	Weak transcription	Primary B cells from cord blood	blood
4	chr3:49509600-49522800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:49509800-49514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:49509800-49514800	Weak transcription	Liver	Liver
9	chr3:49509800-49514800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49509800-49514800	Weak transcription	Colonic Mucosa	Colon
11	chr3:49509800-49514800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:49509800-49520800	Weak transcription	Ovary	ovary
13	chr3:49509800-49522800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:49509800-49522800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:49509800-49522800	Weak transcription	NHEK	skin
16	chr3:49509800-49523000	Weak transcription	Brain Substantia Nigra	brain
17	chr3:49509800-49531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:49510000-49516000	Weak transcription	HSMMtube	muscle
21	chr3:49510000-49520000	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:49510000-49520200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:49510000-49520800	Weak transcription	Right Atrium	heart
24	chr3:49510000-49521200	Weak transcription	HepG2	liver
25	chr3:49510000-49521400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:49510000-49522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:49510000-49523200	Weak transcription	Fetal Kidney	kidney
28	chr3:49510000-49526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:49510000-49535600	Weak transcription	NHLF	lung
30	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:49510200-49516000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:49510800-49517000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:49510800-49518000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:49511000-49518800	Weak transcription	K562	blood
35	chr3:49511400-49518600	Strong transcription	Fetal Intestine Small	intestine
36	chr3:49511400-49522800	Weak transcription	Stomach Mucosa	stomach
37	chr3:49511800-49518200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:49512600-49517000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49512600-49517000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:49513000-49517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:49513200-49517000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:49513400-49514800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:49513400-49514800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:49513400-49515400	Strong transcription	Placenta	Placenta
45	chr3:49513400-49517000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:49513400-49517000	Strong transcription	Fetal Intestine Large	intestine
47	chr3:49513400-49517200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:49513400-49517400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49513600-49514800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:49513600-49515000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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