Variant report

Variant	rs2083127
Chromosome Location	chr3:53916937-53916938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:53914153-53917137	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:53915666-53918109	HepG2	liver:	n/a	n/a
3	MAZ	chr3:53915007-53917351	IMR90	lung:	n/a	chr3:53915928-53915938
4	POLR2A	chr3:53915493-53917518	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:53916773-53917034	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:53915492-53917996	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr3:53915665-53917807	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:53915158-53917310	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:53916626-53916985	GM12892	blood:	n/a	n/a
10	HCFC1	chr3:53915035-53917009	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:53915217-53917615	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:53915515-53917381	GM18505	blood:	n/a	n/a
13	POLR2A	chr3:53914423-53917935	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:53914613-53918608	IMR90	lung:	n/a	n/a
15	POLR2A	chr3:53916878-53917381	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:53915500-53918115	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:53914533-53917912	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:53916837-53917256	K562	blood:	n/a	n/a
19	POLR2A	chr3:53916006-53918522	A549	lung:	n/a	n/a
20	POLR2A	chr3:53915511-53917503	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:53915448-53918024	GM12892	blood:	n/a	n/a
22	POLR2A	chr3:53914664-53917943	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:53915599-53918118	K562	blood:	n/a	n/a
24	POLR2A	chr3:53916779-53917528	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:53915491-53918045	PBDE	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
3	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
4	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
5	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:
6	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000222888	TF binding region
ACTR8	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000113811	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046677	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134092	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1157175	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072145	1.00[ASN][1000 genomes]
rs13315972	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982172	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1992155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276846	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733073	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733081	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816144	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821867	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4569647	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687763	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624599	0.93[ASN][1000 genomes]
rs7636856	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311516	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311518	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822471	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840079	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840362	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9869505	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878207	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878562	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs999514	0.82[ASW][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2083127	IL17RB	cis	parietal	SCAN
rs2083127	ACTR8	cis	lymphoblastoid	seeQTL
rs2083127	ACTR8	cis	cerebellum	SCAN
rs2083127	IL17RB	cis	Artery Tibial	GTEx
rs2083127	CHDH	cis	cerebellum	SCAN
rs2083127	IL17RB	cis	cerebellum	SCAN
rs2083127	RP11-884K10.7	cis	Muscle Skeletal	GTEx
rs2083127	SFMBT1	cis	cerebellum	SCAN
rs2083127	SPATA12	cis	cerebellum	SCAN
rs2083127	ACTR8	cis	parietal	SCAN
rs2083127	IL17RB	cis	Whole Blood	GTEx
rs2083127	ACTR8	cis	Muscle Skeletal	GTEx
rs2083127	ACTR8	cis	Thyroid	GTEx
rs2083127	ACTR8	cis	lung	GTEx
rs2083127	IL17RB	cis	Cerebellum	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53916200-53919400	Weak transcription	Spleen	Spleen
2	chr3:53916200-53924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:53916200-53924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53916600-53917200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:53916600-53917200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:53916600-53917200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:53916600-53917200	Weak transcription	Fetal Stomach	stomach
8	chr3:53916600-53917200	Weak transcription	Pancreas	Pancrea
9	chr3:53916600-53917200	Weak transcription	NHLF	lung
10	chr3:53916600-53917400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:53916600-53917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:53916600-53917600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:53916600-53917600	Weak transcription	Esophagus	oesophagus
14	chr3:53916600-53917600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:53916600-53917600	Weak transcription	Fetal Thymus	thymus
16	chr3:53916600-53917600	Weak transcription	Left Ventricle	heart
17	chr3:53916600-53917800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:53916600-53917800	Weak transcription	Thymus	Thymus
19	chr3:53916600-53917800	Weak transcription	HUVEC	blood vessel
20	chr3:53916600-53918000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:53916600-53918000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:53916600-53918000	Weak transcription	Gastric	stomach
23	chr3:53916600-53918200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:53916600-53918400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:53916600-53918400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:53916600-53918400	Weak transcription	Ovary	ovary
27	chr3:53916600-53918400	Weak transcription	HMEC	breast
28	chr3:53916600-53918600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:53916600-53918600	Weak transcription	Lung	lung
30	chr3:53916600-53918600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:53916600-53918600	Weak transcription	Right Ventricle	heart
32	chr3:53916600-53918800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:53916600-53918800	Weak transcription	Placenta	Placenta
34	chr3:53916600-53919200	Weak transcription	Colonic Mucosa	Colon
35	chr3:53916600-53919400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:53916600-53921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:53916600-53921800	Strong transcription	HSMM	muscle
38	chr3:53916600-53922000	Weak transcription	K562	blood
39	chr3:53916600-53923400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:53916600-53924000	Weak transcription	Psoas Muscle	Psoas
41	chr3:53916600-53924000	Weak transcription	A549	lung
42	chr3:53916600-53924400	Weak transcription	Fetal Kidney	kidney
43	chr3:53916600-53924800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:53916600-53924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:53916600-53924800	Weak transcription	Aorta	Aorta
46	chr3:53916800-53917000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:53916800-53917000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:53916800-53917000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:53916800-53917000	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:53916800-53917000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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