Variant report

Variant	rs11677429
Chromosome Location	chr2:96193061-96193062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr2:96192081-96193078	GM12878	blood:	n/a	n/a
2	MAX	chr2:96192146-96193181	MCF-7	breast:	n/a	chr2:96193011-96193021
3	CTCF	chr2:96192980-96193130	HMEC	breast:	n/a	n/a
4	POLR2A	chr2:96191993-96193076	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:96192044-96193079	GM12878	blood:	n/a	n/a
6	MXI1	chr2:96192028-96193108	IMR90	lung:	n/a	n/a
7	POLR2A	chr2:96191952-96193147	MCF-7	breast:	n/a	n/a
8	MYC	chr2:96192046-96193121	MCF-7	breast:	n/a	chr2:96193011-96193021
9	POLR2A	chr2:96191469-96193210	GM12892	blood:	n/a	n/a
10	MTA3	chr2:96192048-96193064	GM12878	blood:	n/a	n/a
11	RCOR1	chr2:96191730-96193317	IMR90	lung:	n/a	n/a
12	CTCF	chr2:96193060-96193210	GM06990	blood:	n/a	n/a
13	POLR2A	chr2:96191975-96193162	GM12878	blood:	n/a	n/a
14	EBF1	chr2:96192131-96193103	GM12878	blood:	n/a	n/a
15	CHD1	chr2:96191867-96193071	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96192581..96194179-chr2:96218990..96220757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272913	TF binding region
ENSG00000229689	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10874471	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs11164125	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs12468117	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468777	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs12471472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1345917	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1364394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1834135	0.88[EUR][1000 genomes]
rs2216793	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2320170	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2320431	0.86[JPT][hapmap]
rs3755518	0.86[JPT][hapmap]
rs3772031	0.82[YRI][hapmap]
rs3772032	0.82[YRI][hapmap]
rs3772033	0.82[YRI][hapmap]
rs4854251	0.86[JPT][hapmap]
rs4854253	0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4907303	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67628541	0.84[AMR][1000 genomes]
rs72821422	0.87[AMR][1000 genomes]
rs72821437	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869185	0.86[JPT][hapmap]
rs9678800	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv834300	chr2:96087967-96337557	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv1006283	chr2:96159804-96206863	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001305	chr2:96161688-96259200	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1008062	chr2:96166970-96259200	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv998984	chr2:96166970-96290275	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv998587	chr2:96170558-96378228	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv961451	chr2:96176161-96194972	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11677429	AC008268.1	cis	lung	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96191200-96193200	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr2:96191200-96193200	Active TSS	Brain Cingulate Gyrus	brain
3	chr2:96191200-96193600	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:96191200-96193600	Active TSS	HSMM	muscle
5	chr2:96191200-96193800	Active TSS	Fetal Kidney	kidney
6	chr2:96191400-96193200	Active TSS	Fetal Lung	lung
7	chr2:96191400-96193200	Active TSS	HSMMtube	muscle
8	chr2:96191400-96193400	Active TSS	Primary B cells from cord blood	blood
9	chr2:96191400-96193600	Active TSS	Brain Angular Gyrus	brain
10	chr2:96191400-96193600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr2:96191400-96193800	Active TSS	Primary T cells from cord blood	blood
12	chr2:96191400-96194200	Active TSS	GM12878-XiMat	blood
13	chr2:96191600-96193200	Active TSS	Brain Hippocampus Middle	brain
14	chr2:96191600-96193200	Active TSS	Gastric	stomach
15	chr2:96191600-96193400	Active TSS	Colonic Mucosa	Colon
16	chr2:96191600-96193400	Active TSS	Fetal Intestine Large	intestine
17	chr2:96191600-96193600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:96191600-96193600	Active TSS	Brain Anterior Caudate	brain
19	chr2:96191600-96193600	Active TSS	Brain Germinal Matrix	brain
20	chr2:96191600-96193600	Active TSS	Fetal Brain Female	brain
21	chr2:96191600-96193600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr2:96191600-96194600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:96191800-96193200	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr2:96191800-96193200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:96191800-96193200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:96191800-96193200	Active TSS	Brain Substantia Nigra	brain
27	chr2:96191800-96193200	Active TSS	Colon Smooth Muscle	Colon
28	chr2:96191800-96193200	Active TSS	Left Ventricle	heart
29	chr2:96191800-96193200	Active TSS	Placenta Amnion	Placenta Amnion
30	chr2:96191800-96193200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr2:96191800-96193400	Active TSS	Ovary	ovary
32	chr2:96191800-96193400	Active TSS	Right Atrium	heart
33	chr2:96191800-96193600	Active TSS	Psoas Muscle	Psoas
34	chr2:96191800-96193800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:96191800-96193800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:96191800-96194000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:96192000-96193200	Active TSS	Aorta	Aorta
38	chr2:96192000-96193200	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr2:96192000-96193200	Active TSS	NHDF-Ad	bronchial
40	chr2:96192000-96193400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:96192000-96193400	Active TSS	Fetal Stomach	stomach
42	chr2:96192000-96193400	Active TSS	Right Ventricle	heart
43	chr2:96192000-96193600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:96192000-96193600	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr2:96192000-96193600	Active TSS	Stomach Smooth Muscle	stomach
46	chr2:96192000-96193600	Active TSS	NHEK	skin
47	chr2:96192000-96194000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:96192200-96193200	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr2:96192200-96193200	Active TSS	Pancreas	Pancrea
50	chr2:96192200-96193200	Active TSS	Stomach Mucosa	stomach

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