Variant report

Variant	rs11054341
Chromosome Location	chr12:11699795-11699796
allele	A/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	NFIC	chr12:11699706-11700185	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr12:11699741-11699819	GM20000	blood:	n/a	n/a
3	TEAD4	chr12:11699715-11700144	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr12:11699772-11700154	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000247157	TF binding region
ENSG00000221128	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10772486	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12582151	0.89[CHB][hapmap]
rs17817352	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2416791	0.86[ASN][1000 genomes]
rs2416792	0.88[ASN][1000 genomes]
rs4763703	0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs4763705	0.86[ASN][1000 genomes]
rs6488425	0.89[ASN][1000 genomes]
rs6488426	0.90[ASN][1000 genomes]
rs6488427	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6488428	0.87[ASN][1000 genomes]
rs74060996	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956437	0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7960374	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7967647	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11695800-11700000	Enhancers	Fetal Stomach	stomach
2	chr12:11696200-11699800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr12:11696400-11700200	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:11696800-11699800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:11697200-11699800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:11697200-11699800	Weak transcription	Fetal Intestine Small	intestine
7	chr12:11697400-11699800	Enhancers	Primary B cells from peripheral blood	blood
8	chr12:11697400-11708600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:11697800-11700000	Weak transcription	Esophagus	oesophagus
10	chr12:11698200-11699800	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr12:11698200-11699800	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr12:11698200-11700000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr12:11698200-11700000	Enhancers	NH-A	brain
14	chr12:11698200-11700800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr12:11698400-11700000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:11698400-11700000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr12:11698400-11700600	Enhancers	Adipose Nuclei	Adipose
18	chr12:11698600-11700600	Enhancers	Fetal Brain Male	brain
19	chr12:11698800-11699800	Weak transcription	Brain Germinal Matrix	brain
20	chr12:11698800-11699800	Enhancers	Fetal Muscle Leg	muscle
21	chr12:11698800-11699800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:11698800-11700800	Weak transcription	K562	blood
23	chr12:11699000-11699800	Enhancers	Fetal Thymus	thymus
24	chr12:11699000-11699800	Enhancers	Rectal Smooth Muscle	rectum
25	chr12:11699000-11699800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:11699000-11700000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:11699000-11700600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:11699000-11701800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:11699000-11709000	Weak transcription	Fetal Lung	lung
30	chr12:11699200-11699800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:11699200-11699800	Enhancers	Fetal Brain Female	brain
32	chr12:11699200-11699800	Enhancers	Thymus	Thymus
33	chr12:11699200-11700000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:11699200-11700200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:11699200-11700200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:11699200-11700200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:11699200-11701600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:11699400-11699800	Weak transcription	Brain Anterior Caudate	brain
39	chr12:11699400-11700000	Weak transcription	Spleen	Spleen
40	chr12:11699400-11700200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr12:11699400-11700200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr12:11699400-11700400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr12:11699400-11700600	Enhancers	Dnd41	blood
44	chr12:11699400-11700800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:11699400-11707000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:11699600-11699800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:11699600-11700000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:11699600-11700000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:11699600-11700000	Enhancers	GM12878-XiMat	blood
50	chr12:11699600-11700200	Active TSS	Stomach Smooth Muscle	stomach

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