Variant report

Variant	rs1152881
Chromosome Location	chr12:67835533-67835534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67824090..67825052-chr12:67835259..67836288,4	MCF-7	breast:
2	chr12:67835015..67836626-chr12:68041629..68043874,2	MCF-7	breast:
3	chr12:67835312..67836119-chr12:68336837..68337738,4	MCF-7	breast:
4	chr12:67749556..67750279-chr12:67835286..67835947,2	MCF-7	breast:
5	chr12:67835284..67836190-chr12:68017844..68018836,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127334	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11176739	0.81[CEU][hapmap]
rs1161107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161109	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161185	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1161186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4913247	0.81[CEU][hapmap]
rs4913248	0.80[CEU][hapmap]
rs4913249	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs4913323	0.81[CEU][hapmap]
rs4913324	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs7132301	0.81[CEU][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1152881	IFNG	cis	cerebellum	SCAN
rs1152881	TBK1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67830000-67835600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:67830000-67835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:67830000-67836000	Weak transcription	Psoas Muscle	Psoas
4	chr12:67831000-67836600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:67831400-67836000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:67831800-67835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:67834000-67835600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:67835000-67835800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr12:67835000-67836400	Enhancers	GM12878-XiMat	blood
10	chr12:67835000-67836600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr12:67835000-67836800	Enhancers	Stomach Mucosa	stomach
12	chr12:67835000-67837000	Enhancers	Fetal Heart	heart
13	chr12:67835200-67835600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:67835200-67835600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr12:67835200-67835600	Enhancers	Left Ventricle	heart
16	chr12:67835200-67835600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr12:67835200-67835800	Enhancers	NHDF-Ad	bronchial
18	chr12:67835200-67836000	Enhancers	Primary T cells from cord blood	blood
19	chr12:67835200-67836000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:67835200-67836000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr12:67835200-67836200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:67835200-67836200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:67835200-67836400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:67835200-67836400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr12:67835200-67836400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:67835200-67836400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:67835200-67836400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr12:67835200-67836400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:67835200-67836400	Enhancers	Ovary	ovary
30	chr12:67835200-67836400	Enhancers	Rectal Smooth Muscle	rectum
31	chr12:67835200-67836400	Enhancers	Right Atrium	heart
32	chr12:67835200-67836400	Enhancers	NHLF	lung
33	chr12:67835200-67836600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:67835200-67836600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:67835200-67836800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:67835200-67836800	Enhancers	Fetal Intestine Large	intestine
37	chr12:67835200-67836800	Enhancers	Fetal Intestine Small	intestine
38	chr12:67835200-67836800	Enhancers	Fetal Muscle Leg	muscle
39	chr12:67835200-67836800	Enhancers	HSMM	muscle
40	chr12:67835200-67837000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:67835200-67837200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:67835400-67835600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:67835400-67835600	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr12:67835400-67835600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:67835400-67835800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:67835400-67835800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr12:67835400-67835800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr12:67835400-67835800	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr12:67835400-67835800	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr12:67835400-67836000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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