Variant report

Variant	rs835632
Chromosome Location	chr3:136676525-136676526
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:136676334-136677059	MCF10A-Er-Src	breast:	n/a	chr3:136676620-136676629
2	STAT3	chr3:136676451-136677158	MCF10A-Er-Src	breast:	n/a	chr3:136676611-136676619
3	SP1	chr3:136676375-136677139	HCT-116	colon:	n/a	chr3:136676611-136676632
4	POLR2A	chr3:136675938-136679061	MCF10A-Er-Src	breast:	n/a	n/a
5	RFX5	chr3:136676433-136676972	Hela-S3	cervix:	n/a	chr3:136676621-136676630
6	TBP	chr3:136676509-136676856	K562	blood:	n/a	n/a
7	CEBPB	chr3:136676498-136677863	Hela-S3	cervix:	n/a	chr3:136676622-136676630
8	RAD21	chr3:136676518-136676966	Hela-S3	cervix:	n/a	n/a
9	BRCA1	chr3:136676499-136677086	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:136676098-136677906	K562	blood:	n/a	n/a
11	ATF3	chr3:136676420-136677089	HCT-116	colon:	n/a	n/a
12	STAT3	chr3:136676522-136677010	MCF10A-Er-Src	breast:	n/a	chr3:136676611-136676619
13	STAT3	chr3:136676215-136676879	MCF10A-Er-Src	breast:	n/a	chr3:136676611-136676619
14	JUND	chr3:136676517-136677047	K562	blood:	n/a	chr3:136676620-136676629
15	RCOR1	chr3:136676488-136677057	K562	blood:	n/a	n/a
16	EP300	chr3:136676489-136677973	Hela-S3	cervix:	n/a	n/a
17	MYC	chr3:136676516-136676981	K562	blood:	n/a	n/a
18	TBP	chr3:136676395-136677172	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr3:136676445-136677045	Hela-S3	cervix:	n/a	n/a
20	MAX	chr3:136676525-136677051	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:136676462-136677039	HCT-116	colon:	n/a	n/a
22	RCOR1	chr3:136676398-136677153	Hela-S3	cervix:	n/a	n/a
23	ZKSCAN1	chr3:136676521-136676959	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr3:136676415-136677146	HCT-116	colon:	n/a	chr3:136676622-136676630
25	FOS	chr3:136676477-136676954	MCF10A-Er-Src	breast:	n/a	chr3:136676620-136676629
26	FOS	chr3:136676477-136676949	MCF10A-Er-Src	breast:	n/a	chr3:136676620-136676629
27	CEBPB	chr3:136676485-136677085	HCT-116	colon:	n/a	chr3:136676622-136676630
28	E2F4	chr3:136676481-136676934	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:136676510-136677172	U87	brain:	n/a	n/a
30	STAT3	chr3:136676490-136676912	MCF10A-Er-Src	breast:	n/a	chr3:136676611-136676619
31	ATF3	chr3:136676491-136676984	K562	blood:	n/a	n/a
32	EP300	chr3:136676506-136676997	K562	blood:	n/a	n/a
33	POLR2A	chr3:136676456-136676985	HCT-116	colon:	n/a	n/a
34	POLR2A	chr3:136676478-136677278	Hela-S3	cervix:	n/a	n/a
35	MYC	chr3:136676508-136677530	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr3:136676470-136677265	K562	blood:	n/a	n/a
37	TEAD4	chr3:136676447-136676938	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136470409..136473181-chr3:136674963..136676647,2	K562	blood:

Variant related genes	Relation type
IL20RB	TF binding region
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10935213	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935214	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1097288	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12054218	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12054220	0.82[LWK][hapmap]
rs12054408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486911	0.84[CEU][hapmap]
rs12494558	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624703	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654904	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654923	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654925	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654926	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682333	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1682337	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682356	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1682357	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844325	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16844326	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844362	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168635	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2163896	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35289288	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361237	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361239	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361241	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361242	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361243	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361244	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361245	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361248	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361250	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361251	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs361252	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs747842	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747843	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs75976	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs75977	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835633	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835637	0.85[CEU][hapmap]
rs835641	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835642	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835649	0.85[CEU][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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs835632	SPSB4	cis	cerebellum	SCAN
rs835632	PCCB	cis	cerebellum	SCAN
rs835632	PCCB	cis	parietal	SCAN
rs835632	TMEM22	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136656400-136681400	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:136658600-136679400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:136662000-136676600	Weak transcription	Psoas Muscle	Psoas
4	chr3:136662800-136678800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:136665200-136676800	Weak transcription	Aorta	Aorta
6	chr3:136665200-136680200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:136665400-136679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:136665400-136680200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:136665400-136680200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:136665600-136680000	Weak transcription	Dnd41	blood
11	chr3:136665600-136689400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:136666600-136680400	Weak transcription	Left Ventricle	heart
13	chr3:136669400-136680200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:136670000-136676600	Enhancers	Hela-S3	cervix
15	chr3:136670600-136676600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:136670600-136676800	Enhancers	HMEC	breast
17	chr3:136671600-136676600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:136671800-136676600	Enhancers	NHEK	skin
19	chr3:136673200-136676800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:136673400-136676600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:136673600-136676600	Enhancers	K562	blood
22	chr3:136673800-136680400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:136674000-136680200	Weak transcription	Fetal Thymus	thymus
24	chr3:136674200-136679800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:136674200-136680200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:136674400-136676600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:136674400-136677600	Weak transcription	Thymus	Thymus
28	chr3:136674600-136677000	Weak transcription	Primary T cells from cord blood	blood
29	chr3:136674600-136680000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:136674800-136676800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:136674800-136677000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:136674800-136680200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:136675000-136676600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:136675000-136679800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:136675200-136677000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:136675400-136676800	Enhancers	NHDF-Ad	bronchial
37	chr3:136675400-136677000	Enhancers	NHLF	lung
38	chr3:136675400-136677800	Weak transcription	NH-A	brain
39	chr3:136675600-136676600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:136675600-136676600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:136675600-136676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:136675600-136677600	Weak transcription	Esophagus	oesophagus
43	chr3:136675600-136678200	Enhancers	A549	lung
44	chr3:136675600-136679400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:136675600-136679600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:136675600-136679800	Weak transcription	Osteobl	bone
47	chr3:136675600-136681200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:136675800-136679600	Weak transcription	HSMM	muscle
49	chr3:136676000-136676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:136676000-136678600	Weak transcription	Small Intestine	intestine

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