Variant report

Variant	rs9789521
Chromosome Location	chr2:153506994-153506995
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153506812..153508421-chr2:153573879..153576472,2	K562	blood:
2	chr2:153505525..153507325-chr2:153525250..153527752,2	K562	blood:
3	chr2:153498882..153503478-chr2:153504081..153508204,8	K562	blood:
4	chr2:153506687..153509225-chr2:153511022..153513824,2	K562	blood:

Variant related genes	Relation type
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10172024	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs10181485	0.89[ASN][1000 genomes]
rs10200667	0.87[ASN][1000 genomes]
rs1036526	0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs1065266	0.80[CHB][hapmap];0.91[CHD][hapmap];0.89[ASN][1000 genomes]
rs10931229	0.80[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1128804	0.85[CHD][hapmap];0.80[JPT][hapmap]
rs11544718	0.89[ASN][1000 genomes]
rs11899051	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12477881	0.83[ASN][1000 genomes]
rs12621561	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs12693415	0.85[CHB][hapmap]
rs12997814	0.89[ASN][1000 genomes]
rs13005368	0.87[ASN][1000 genomes]
rs13010731	0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs13017428	0.87[ASN][1000 genomes]
rs13031469	0.90[ASN][1000 genomes]
rs13419068	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1370498	0.80[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs1437678	0.80[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs16831548	0.80[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs16831740	0.88[CHD][hapmap];0.80[JPT][hapmap]
rs17328734	0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs17400645	0.92[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962313	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1986743	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1992146	0.80[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2118377	0.80[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs2304556	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs2304559	0.89[ASN][1000 genomes]
rs2346534	0.89[ASN][1000 genomes]
rs2346539	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2346540	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346541	0.87[ASN][1000 genomes]
rs2346542	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2346543	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346549	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2346550	0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs3171980	0.80[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs3175	0.91[CHD][hapmap];0.95[JPT][hapmap]
rs34668102	0.89[ASN][1000 genomes]
rs3748937	0.96[ASN][1000 genomes]
rs3748938	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3748939	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs3762503	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762506	0.89[ASN][1000 genomes]
rs3762507	0.80[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs3811566	0.87[ASN][1000 genomes]
rs4233660	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4267470	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4580346	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664121	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4664122	0.80[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs4664601	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664602	0.85[ASN][1000 genomes]
rs4664604	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs4664605	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4664606	0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4664607	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs4664609	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4664610	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61049574	0.88[ASN][1000 genomes]
rs6434128	0.84[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[ASN][1000 genomes]
rs6434161	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs6434162	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs6713779	0.89[ASN][1000 genomes]
rs6723574	0.92[ASN][1000 genomes]
rs6727279	0.97[ASN][1000 genomes]
rs6744923	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746079	0.98[ASN][1000 genomes]
rs6746321	0.89[ASN][1000 genomes]
rs6748160	0.90[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs715047	0.83[ASN][1000 genomes]
rs72871191	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72872607	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556673	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7558920	0.94[ASN][1000 genomes]
rs7559219	0.87[ASN][1000 genomes]
rs7560393	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs7570759	0.87[ASN][1000 genomes]
rs7576152	0.83[ASN][1000 genomes]
rs7576847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7582253	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7589899	0.80[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7592669	0.87[ASN][1000 genomes]
rs7593347	0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs7596408	0.90[CHB][hapmap]
rs7599946	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7605709	0.87[ASN][1000 genomes]
rs7608603	0.89[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs9288121	0.80[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs9288125	0.80[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs9288127	0.89[ASN][1000 genomes]
rs9646744	0.87[ASN][1000 genomes]
rs9789505	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9789521	NR4A2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153469000-153509800	Weak transcription	Small Intestine	intestine
2	chr2:153471000-153507000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:153492000-153508200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:153492400-153513400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:153495400-153517400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:153497000-153531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:153497200-153514000	Weak transcription	Colonic Mucosa	Colon
9	chr2:153497200-153521200	Weak transcription	Esophagus	oesophagus
10	chr2:153497400-153516200	Weak transcription	Spleen	Spleen
11	chr2:153498200-153507000	Weak transcription	HUVEC	blood vessel
12	chr2:153498400-153512200	Weak transcription	Thymus	Thymus
13	chr2:153499000-153507600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:153499800-153507200	Weak transcription	Primary T cells from cord blood	blood
15	chr2:153500000-153512200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:153500400-153517200	Weak transcription	Hela-S3	cervix
17	chr2:153500800-153509800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:153501200-153508400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:153501400-153531800	Weak transcription	Aorta	Aorta
20	chr2:153502200-153508400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:153502600-153507200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:153502600-153507200	Weak transcription	GM12878-XiMat	blood
23	chr2:153503000-153510600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:153503200-153507000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:153503200-153508400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:153503200-153512200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:153503400-153509800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:153503400-153512800	Weak transcription	Fetal Stomach	stomach
29	chr2:153503600-153512400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:153503800-153514600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:153504200-153507600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:153504400-153508200	Weak transcription	HSMM	muscle
33	chr2:153504400-153508600	Weak transcription	Fetal Lung	lung
34	chr2:153504400-153538200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:153504600-153508600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:153504600-153508600	Weak transcription	K562	blood
37	chr2:153504600-153512200	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:153504600-153512800	Weak transcription	Lung	lung
39	chr2:153504600-153513600	Weak transcription	Fetal Kidney	kidney
40	chr2:153504600-153514800	Weak transcription	Fetal Heart	heart
41	chr2:153504600-153516000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:153504800-153508400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:153504800-153508800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:153504800-153512200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:153505000-153507400	Weak transcription	Left Ventricle	heart
46	chr2:153505000-153508000	Weak transcription	NH-A	brain
47	chr2:153505000-153508800	Weak transcription	Osteobl	bone
48	chr2:153505000-153509200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:153505000-153509200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:153505000-153510000	Weak transcription	Muscle Satellite Cultured Cells	--

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