Variant report

Variant	rs10934557
Chromosome Location	chr3:121412394-121412395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121410605..121412788-chr3:121413603..121415735,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10511407	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs10934556	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934561	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs11915822	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927625	0.81[YRI][hapmap]
rs12486456	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12488717	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489110	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489196	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489686	1.00[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs12491109	1.00[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs12491671	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491714	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12492214	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12492861	1.00[CEU][hapmap]
rs12493927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629720	1.00[CEU][hapmap]
rs12631803	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12637265	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321798	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs1574654	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1814668	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1919553	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919554	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.85[ASN][1000 genomes]
rs1919556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920307	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs1971281	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2055034	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2689278	1.00[CEU][hapmap]
rs2700413	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2700414	0.82[JPT][hapmap]
rs35674179	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825165	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805125	1.00[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs3805129	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs3966063	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4048693	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271407	0.87[EUR][1000 genomes]
rs4610269	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4676761	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs55930520	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964762	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109033	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56286202	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438681	1.00[CEU][hapmap]
rs6762575	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766737	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775634	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786605	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793556	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798575	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620562	0.91[CEU][hapmap]
rs7625960	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7626052	1.00[CEU][hapmap]
rs7640859	0.81[CEU][hapmap]
rs7643293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7650341	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs9834185	1.00[CEU][hapmap]
rs9869891	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv980073	chr3:121409447-121412574	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10934557	IQCB1	cis	lymphoblastoid	seeQTL
rs10934557	HCLS1	cis	lymphoblastoid	seeQTL
rs10934557	PARP14	cis	cerebellum	SCAN
rs10934557	HCLS1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
2	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
4	chr3:121399000-121415400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:121399000-121425400	Weak transcription	Pancreas	Pancrea
6	chr3:121399000-121426400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:121399000-121440400	Weak transcription	K562	blood
8	chr3:121399200-121416800	Weak transcription	Fetal Stomach	stomach
9	chr3:121401200-121416800	Weak transcription	Spleen	Spleen
10	chr3:121401200-121429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:121401200-121434000	Weak transcription	Gastric	stomach
12	chr3:121403800-121414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
14	chr3:121407400-121429400	Weak transcription	Esophagus	oesophagus
15	chr3:121408200-121417400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:121408200-121422400	Strong transcription	Placenta	Placenta
17	chr3:121408200-121428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:121408400-121413000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:121408400-121421000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:121408400-121421600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:121408600-121412800	Strong transcription	Fetal Thymus	thymus
22	chr3:121408600-121413000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:121408600-121413200	Strong transcription	Fetal Intestine Large	intestine
24	chr3:121408600-121413800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:121408600-121414000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:121408600-121414000	Strong transcription	NH-A	brain
27	chr3:121408600-121414600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:121408600-121414600	Strong transcription	Liver	Liver
29	chr3:121408600-121414800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:121408600-121417600	Strong transcription	Fetal Brain Female	brain
31	chr3:121408600-121417600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:121408600-121417800	Strong transcription	HSMMtube	muscle
33	chr3:121408600-121418200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:121408600-121420400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:121408600-121421400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:121408600-121421600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:121408600-121421600	Strong transcription	Primary T cells from cord blood	blood
38	chr3:121408600-121421800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:121408600-121421800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:121408600-121422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:121408600-121424600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:121408600-121424800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:121408600-121424800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr3:121408600-121427400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:121408600-121428200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:121408800-121415800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:121408800-121422800	Strong transcription	Primary B cells from cord blood	blood
48	chr3:121408800-121424800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:121409000-121412600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:121409000-121414400	Strong transcription	Primary hematopoietic stem cells	blood

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