Variant report

Variant	rs11710169
Chromosome Location	chr3:121426655-121426656
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	chr3:121420842..121422524-chr3:121426480..121428817,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10470410	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12695415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075324	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2141615	0.84[MEX][hapmap]
rs28497949	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34051021	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34492106	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805134	0.83[MEX][hapmap]
rs56382357	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7340674	0.92[CEU][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs9817555	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819530	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11710169	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs11710169	CHST13	cis	cerebellum	SCAN
rs11710169	MUC13	cis	cerebellum	SCAN
rs11710169	IQCB1	cis	parietal	SCAN
rs11710169	SLC15A2	cis	cerebellum	SCAN
rs11710169	CCDC58	cis	parietal	SCAN
rs11710169	SLC15A2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:121396800-121435600	Weak transcription	Psoas Muscle	Psoas
3	chr3:121399000-121440400	Weak transcription	K562	blood
4	chr3:121401200-121429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:121401200-121434000	Weak transcription	Gastric	stomach
6	chr3:121404000-121432800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:121407400-121429400	Weak transcription	Esophagus	oesophagus
8	chr3:121408200-121428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:121408600-121427400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:121408600-121428200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:121410400-121435600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:121411000-121432000	Weak transcription	NHEK	skin
13	chr3:121411000-121432800	Weak transcription	Fetal Brain Male	brain
14	chr3:121411000-121442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:121411400-121432800	Weak transcription	Colonic Mucosa	Colon
16	chr3:121411400-121437200	Weak transcription	Small Intestine	intestine
17	chr3:121413400-121446200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:121414200-121428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:121414800-121436200	Weak transcription	Stomach Mucosa	stomach
20	chr3:121415400-121427400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:121415600-121428400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:121417200-121430800	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:121417200-121435800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:121417400-121431600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:121417600-121430800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:121417600-121431600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:121417600-121432000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:121417600-121432000	Weak transcription	Fetal Brain Female	brain
29	chr3:121417600-121432800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:121417600-121432800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:121417600-121434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:121417600-121434200	Weak transcription	Aorta	Aorta
33	chr3:121417600-121435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:121417600-121437200	Weak transcription	Spleen	Spleen
35	chr3:121417800-121431600	Weak transcription	HSMMtube	muscle
36	chr3:121418000-121432000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:121418000-121434200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:121418000-121435400	Weak transcription	NHLF	lung
39	chr3:121418800-121442000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:121419600-121436200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:121419800-121434400	Weak transcription	HUVEC	blood vessel
42	chr3:121420200-121432600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:121420200-121433000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:121420400-121432000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:121420600-121429400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:121420800-121430800	Weak transcription	Fetal Kidney	kidney
47	chr3:121420800-121432000	Weak transcription	Brain Germinal Matrix	brain
48	chr3:121421000-121426800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:121421000-121430800	Weak transcription	NH-A	brain
50	chr3:121421000-121431200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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