Variant report

Variant	rs2881900
Chromosome Location	chr3:138549009-138549010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138548916..138550963-chr3:138596429..138598640,2	K562	blood:
2	chr3:138547576..138550266-chr3:138633999..138636358,2	MCF-7	breast:
3	chr3:138535838..138538762-chr3:138546948..138549872,2	K562	blood:
4	chr3:138521559..138523746-chr3:138548742..138551638,2	K562	blood:
5	chr3:138532061..138535019-chr3:138545611..138549640,3	K562	blood:
6	chr3:138541873..138544767-chr3:138546803..138549506,3	K562	blood:

Variant related genes	Relation type
ENSG00000241429	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1068685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10804659	0.89[EUR][1000 genomes]
rs10935288	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705762	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706016	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11708762	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	0.81[EUR][1000 genomes]
rs11711360	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.83[EUR][1000 genomes]
rs11720178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11924479	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.83[EUR][1000 genomes]
rs12497815	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631035	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633714	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs13061496	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs13072146	0.81[EUR][1000 genomes]
rs13077455	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082808	0.84[EUR][1000 genomes]
rs1400266	0.83[EUR][1000 genomes]
rs1663554	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1673597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17484361	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs191775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2197387	0.81[EUR][1000 genomes]
rs2607796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28408150	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35214574	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs361054	0.80[EUR][1000 genomes]
rs361057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs361067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs361068	0.81[EUR][1000 genomes]
rs361071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs361072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs361080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs361081	0.80[EUR][1000 genomes]
rs361082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs361083	0.81[EUR][1000 genomes]
rs361084	0.81[EUR][1000 genomes]
rs361087	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361088	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs361096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs371762	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs385254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs398065	0.82[EUR][1000 genomes]
rs404110	0.81[EUR][1000 genomes]
rs413147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4305444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs439720	0.81[EUR][1000 genomes]
rs4405948	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473388	0.81[EUR][1000 genomes]
rs476800	0.81[EUR][1000 genomes]
rs482334	0.82[EUR][1000 genomes]
rs4894350	0.81[EUR][1000 genomes]
rs4894351	0.81[EUR][1000 genomes]
rs4894352	0.81[EUR][1000 genomes]
rs4894353	0.81[EUR][1000 genomes]
rs4894354	0.80[EUR][1000 genomes]
rs4894358	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894359	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.81[EUR][1000 genomes]
rs493152	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs497900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs500687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs511207	0.81[EUR][1000 genomes]
rs520904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs524164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs531577	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs539619	0.82[EUR][1000 genomes]
rs540198	0.81[EUR][1000 genomes]
rs558905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs559160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs564455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs600590	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs601032	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs603723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs607044	0.81[EUR][1000 genomes]
rs62282169	0.83[EUR][1000 genomes]
rs624099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs635592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6439817	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs647972	0.81[EUR][1000 genomes]
rs6773514	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776585	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6780989	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791627	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794270	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800801	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801207	0.83[EUR][1000 genomes]
rs6810351	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7612106	0.84[EUR][1000 genomes]
rs7613579	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628172	0.88[EUR][1000 genomes]
rs7643722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7646689	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650967	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs772612	0.80[EUR][1000 genomes]
rs773045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9289566	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813576	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817727	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818354	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821694	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9822500	0.86[EUR][1000 genomes]
rs9822714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9832012	0.81[EUR][1000 genomes]
rs9834963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9851887	0.81[EUR][1000 genomes]
rs9855727	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9877108	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv967072	chr3:138543196-138550847	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2881900	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs2881900	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs2881900	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138504000-138552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:138506000-138551800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:138528800-138552600	Weak transcription	Colonic Mucosa	Colon
4	chr3:138535200-138551600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:138537000-138552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:138537200-138552000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:138537200-138552200	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:138537400-138551400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:138537400-138552200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:138537600-138551200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:138537600-138551400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:138537600-138551400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:138537600-138552000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:138537600-138552200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:138537600-138552200	Weak transcription	Brain Substantia Nigra	brain
16	chr3:138537600-138552400	Weak transcription	Brain Angular Gyrus	brain
17	chr3:138537600-138552400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:138537600-138552600	Weak transcription	Ovary	ovary
19	chr3:138539200-138551200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:138539200-138552200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:138543000-138552200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:138543200-138552200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:138543200-138552400	Weak transcription	Fetal Stomach	stomach
24	chr3:138543400-138550800	Weak transcription	Hela-S3	cervix
25	chr3:138543400-138552000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:138543400-138552200	Weak transcription	HMEC	breast
27	chr3:138543400-138552400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:138543400-138552600	Weak transcription	HSMM	muscle
29	chr3:138543600-138552200	Weak transcription	HUVEC	blood vessel
30	chr3:138543600-138552400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:138543600-138552400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:138543800-138550800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:138543800-138552200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:138544400-138552200	Weak transcription	A549	lung
35	chr3:138544600-138550600	Weak transcription	Fetal Brain Female	brain
36	chr3:138544600-138552200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:138544800-138552000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:138544800-138552000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:138544800-138552200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:138544800-138552200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:138544800-138552200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:138544800-138552200	Weak transcription	Fetal Kidney	kidney
43	chr3:138544800-138552400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:138544800-138552400	Weak transcription	Lung	lung
45	chr3:138544800-138552600	Weak transcription	Gastric	stomach
46	chr3:138544800-138552600	Weak transcription	Spleen	Spleen
47	chr3:138545000-138550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:138545000-138550600	Weak transcription	Fetal Intestine Large	intestine
49	chr3:138545000-138550800	Weak transcription	NHEK	skin
50	chr3:138545000-138551200	Weak transcription	Thymus	Thymus

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