Variant report

Variant	rs261877
Chromosome Location	chr12:32446835-32446836
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	chr12:32445285..32448075-chr12:32450808..32453523,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1151038	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1151039	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs1151045	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1239401	0.81[YRI][hapmap]
rs161981	0.82[JPT][hapmap]
rs185487	0.82[JPT][hapmap]
rs2129590	0.81[ASW][hapmap];0.82[JPT][hapmap]
rs2594000	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs261869	0.82[JPT][hapmap]
rs261870	0.82[JPT][hapmap]
rs261871	0.88[YRI][hapmap]
rs261874	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs261875	0.95[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs261876	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2632344	0.82[JPT][hapmap]
rs2632359	0.91[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs2650137	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2728704	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2728705	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs708225	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708226	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708227	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs751720	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs753296	0.81[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs792473	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs792474	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs792863	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs806784	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs813784	0.83[CEU][hapmap]
rs814243	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs901598	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs261877	TNFSF13	trans	lymphoblastoid	seeQTL
rs261877	TNFSF12-TNFSF13	trans	lymphoblastoid	seeQTL
rs261877	IFI44L	trans	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32427000-32458600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:32427000-32459400	Weak transcription	Aorta	Aorta
3	chr12:32427000-32463000	Weak transcription	NHLF	lung
4	chr12:32427200-32463000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:32427600-32454400	Weak transcription	Primary B cells from cord blood	blood
6	chr12:32435200-32448200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:32438200-32449600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:32438800-32449600	Weak transcription	Fetal Brain Female	brain
9	chr12:32439800-32447000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:32440200-32458600	Weak transcription	Thymus	Thymus
11	chr12:32441000-32448800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:32442400-32451800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:32443400-32461000	Weak transcription	Primary T cells from cord blood	blood
14	chr12:32443600-32448200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:32443600-32449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:32443600-32454000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:32443600-32458600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:32443600-32458600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:32443600-32458600	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:32443600-32458600	Weak transcription	NH-A	brain
21	chr12:32443600-32458800	Weak transcription	HMEC	breast
22	chr12:32443600-32461200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:32443600-32463200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:32443600-32465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:32443800-32447200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:32443800-32448000	Weak transcription	HSMMtube	muscle
27	chr12:32443800-32449600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:32443800-32450800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:32443800-32451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:32443800-32451800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:32443800-32452000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:32443800-32452200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:32443800-32458400	Weak transcription	HSMM	muscle
34	chr12:32443800-32458600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:32443800-32458600	Weak transcription	Ovary	ovary
36	chr12:32443800-32460200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:32443800-32464600	Weak transcription	NHDF-Ad	bronchial
38	chr12:32443800-32464800	Weak transcription	Brain Substantia Nigra	brain
39	chr12:32443800-32480400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:32444000-32449000	Weak transcription	A549	lung
41	chr12:32444000-32460600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:32444200-32465000	Weak transcription	Hela-S3	cervix
43	chr12:32445200-32456000	Weak transcription	Dnd41	blood
44	chr12:32445200-32458800	Weak transcription	Fetal Stomach	stomach
45	chr12:32445400-32464000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:32445600-32458600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:32445600-32463600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:32445800-32447200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:32445800-32464800	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:32446000-32461600	Weak transcription	Stomach Smooth Muscle	stomach

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