Variant report

Variant	rs2553427
Chromosome Location	chr3:101106527-101106528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101105681..101107819-chr3:101109398..101112235,3	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1019677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs10936607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936642	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10936664	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491955	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12496260	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13087404	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088318	0.91[CEU][hapmap]
rs13089177	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13089552	0.86[ASN][1000 genomes]
rs13320918	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13322987	0.95[EUR][1000 genomes]
rs16843927	1.00[CEU][hapmap];0.90[YRI][hapmap];0.96[EUR][1000 genomes]
rs1918405	0.90[EUR][1000 genomes]
rs2141179	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2141180	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];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178036	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2250611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317699	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317700	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317749	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317751	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553424	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682383	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682391	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28460520	0.81[EUR][1000 genomes]
rs28565548	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34255148	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs348866	0.83[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs348869	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs3846091	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4287896	0.90[EUR][1000 genomes]
rs4456838	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4524254	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[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];1.00[ASN][1000 genomes]
rs4683917	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683918	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs473702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487623	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs497953	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503734	0.83[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs508537	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs520558	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533852	0.83[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs551442	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280667	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441602	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441608	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[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];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441610	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771561	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772703	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes]
rs6773536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628681	0.90[EUR][1000 genomes]
rs7631506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes]
rs7636475	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814991	0.91[EUR][1000 genomes]
rs9843186	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9856435	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9859077	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870114	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9874188	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2553427	ZNF447	trans	multi-tissue	Pritchard
rs2553427	FAM172B	cis	parietal	SCAN
rs2553427	ZNF329	trans	multi-tissue	Pritchard
rs2553427	SENP7	Cis_1M	lymphoblastoid	RTeQTL
rs2553427	ZNF274	trans	multi-tissue	Pritchard
rs2553427	ZNF671	trans	multi-tissue	Pritchard
rs2553427	ZNF256	trans	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101039800-101106600	Weak transcription	Thymus	Thymus
2	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:101084600-101106600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:101085000-101106600	Weak transcription	Fetal Brain Female	brain
5	chr3:101085600-101106800	Weak transcription	Dnd41	blood
6	chr3:101085600-101137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:101090600-101106600	Weak transcription	Fetal Lung	lung
8	chr3:101091000-101106800	Weak transcription	Fetal Thymus	thymus
9	chr3:101096800-101106600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:101096800-101111600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:101097600-101108000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:101099000-101108000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:101099000-101110400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:101099000-101114600	Weak transcription	K562	blood
15	chr3:101099600-101106800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:101099600-101107000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:101099600-101107000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:101099600-101107200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:101099600-101107800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr3:101100200-101106600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:101100800-101108200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:101101200-101106600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:101101200-101108000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:101102000-101106800	Enhancers	Left Ventricle	heart
25	chr3:101102600-101106800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:101102600-101107600	Strong transcription	Primary T cells from cord blood	blood
27	chr3:101103400-101106600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:101104200-101106600	Enhancers	Right Atrium	heart
29	chr3:101104200-101106800	Enhancers	Right Ventricle	heart
30	chr3:101104600-101106600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:101104600-101108000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:101104800-101106600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:101105000-101106800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:101105200-101106600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:101105400-101107200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:101105400-101107200	Enhancers	Gastric	stomach
37	chr3:101105600-101106600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:101105600-101106600	Enhancers	Lung	lung
39	chr3:101105600-101106800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:101105600-101106800	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:101105600-101107000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:101105600-101107000	Enhancers	Esophagus	oesophagus
43	chr3:101105600-101107400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:101105800-101107000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:101105800-101107200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:101106000-101106800	Weak transcription	Ovary	ovary
47	chr3:101106000-101107200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:101106000-101107200	ZNF genes & repeats	Fetal Stomach	stomach
49	chr3:101106000-101111200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:101106000-101111400	Weak transcription	Stomach Smooth Muscle	stomach

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