Variant report

Variant	rs3812879
Chromosome Location	chr13:39625278-39625279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39625131..39625918-chr13:39837190..39837917,2	MCF-7	breast:
2	chr13:39625072..39625743-chr13:39719158..39719753,2	MCF-7	breast:
3	chr13:39624114..39626066-chr13:39636709..39639010,2	K562	blood:
4	chr13:39611994..39615233-chr13:39623870..39626918,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1109625	0.85[CEU][hapmap]
rs11147745	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12428445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12429324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12429338	0.85[ASN][1000 genomes]
rs12430450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12431316	0.84[ASN][1000 genomes]
rs1326405	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17058947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17058990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17059014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2094252	0.84[ASN][1000 genomes]
rs2094253	0.84[ASN][1000 genomes]
rs2094254	0.84[ASN][1000 genomes]
rs2104518	0.84[ASN][1000 genomes]
rs2274384	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2274385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2296648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34316151	0.84[ASN][1000 genomes]
rs34327528	0.84[ASN][1000 genomes]
rs35804724	0.89[ASN][1000 genomes]
rs35864330	0.84[ASN][1000 genomes]
rs3751377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3751378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3751379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4142398	0.99[ASN][1000 genomes]
rs55809136	0.89[ASN][1000 genomes]
rs66496062	0.84[ASN][1000 genomes]
rs66908302	0.83[ASN][1000 genomes]
rs67296293	0.83[ASN][1000 genomes]
rs73169457	0.84[ASN][1000 genomes]
rs7317852	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7318688	0.89[ASN][1000 genomes]
rs7327748	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs747752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7987207	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7994530	0.97[ASN][1000 genomes]
rs7997052	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs7998475	0.84[ASN][1000 genomes]
rs8000929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9566389	0.85[ASN][1000 genomes]
rs9566391	0.89[ASN][1000 genomes]
rs9566393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566396	0.99[ASN][1000 genomes]
rs9566397	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576666	0.85[CEU][hapmap]
rs9576669	0.85[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap]
rs9576670	0.83[ASN][1000 genomes]
rs9576673	0.81[ASN][1000 genomes]
rs9576674	0.83[ASN][1000 genomes]
rs9576676	0.83[ASN][1000 genomes]
rs9576677	0.83[ASN][1000 genomes]
rs9576678	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9576679	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs9576681	0.84[ASN][1000 genomes]
rs9576683	0.84[ASN][1000 genomes]
rs9576684	0.84[ASN][1000 genomes]
rs9576685	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9576686	0.84[ASN][1000 genomes]
rs9576688	0.84[ASN][1000 genomes]
rs9576690	0.83[ASN][1000 genomes]
rs9576692	0.84[ASN][1000 genomes]
rs9576693	0.82[ASN][1000 genomes]
rs9576695	0.84[ASN][1000 genomes]
rs9576696	0.85[ASN][1000 genomes]
rs9576697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9576698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9576699	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9576700	0.85[ASN][1000 genomes]
rs9576701	0.89[ASN][1000 genomes]
rs9576703	0.87[ASN][1000 genomes]
rs9576705	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9576707	0.89[ASN][1000 genomes]
rs9576710	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9576711	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9576717	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1035255	chr13:39618302-39715336	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3812879	C13orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39613000-39629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:39613000-39636200	Weak transcription	Spleen	Spleen
3	chr13:39613200-39626600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:39613200-39636400	Weak transcription	Gastric	stomach
5	chr13:39613200-39637200	Weak transcription	Pancreas	Pancrea
6	chr13:39613200-39647000	Weak transcription	Left Ventricle	heart
7	chr13:39613200-39647200	Weak transcription	Lung	lung
8	chr13:39613400-39646600	Weak transcription	Aorta	Aorta
9	chr13:39613600-39626600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:39613600-39626600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr13:39613600-39629000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:39613600-39629200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr13:39613600-39629800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr13:39613800-39627000	Weak transcription	Brain Substantia Nigra	brain
15	chr13:39613800-39639200	Weak transcription	Fetal Stomach	stomach
16	chr13:39614000-39625400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:39614000-39627000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr13:39614000-39627000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:39614000-39628400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:39614000-39634400	Weak transcription	Fetal Kidney	kidney
21	chr13:39614400-39644000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr13:39615000-39625800	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:39615000-39626600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr13:39615000-39627000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr13:39615000-39628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:39615000-39629800	Weak transcription	Brain Germinal Matrix	brain
27	chr13:39615000-39634400	Weak transcription	Fetal Brain Male	brain
28	chr13:39615000-39636200	Weak transcription	Fetal Intestine Small	intestine
29	chr13:39615000-39638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:39615200-39627000	Weak transcription	K562	blood
31	chr13:39615200-39631600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr13:39615200-39637600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr13:39615400-39627800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr13:39617200-39628800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr13:39618200-39629200	Weak transcription	NHDF-Ad	bronchial
36	chr13:39618600-39643800	Weak transcription	Ovary	ovary
37	chr13:39618800-39626600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr13:39618800-39627000	Weak transcription	NHEK	skin
39	chr13:39619000-39626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:39619200-39627000	Weak transcription	Brain Anterior Caudate	brain
41	chr13:39619200-39631800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr13:39619400-39626800	Weak transcription	Brain Hippocampus Middle	brain
43	chr13:39619600-39627600	Weak transcription	Fetal Brain Female	brain
44	chr13:39619600-39632600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:39619800-39626400	Weak transcription	Dnd41	blood
46	chr13:39619800-39626800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr13:39619800-39629600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr13:39619800-39629600	Weak transcription	Placenta	Placenta
49	chr13:39620000-39633600	Weak transcription	GM12878-XiMat	blood
50	chr13:39620000-39644200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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