Variant report

Variant	rs6545946
Chromosome Location	chr2:62713533-62713534
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	NFIC	chr2:62712905-62713785	SK-N-SH	brain:	n/a	chr2:62713431-62713447
2	TCF12	chr2:62712789-62713865	SK-N-SH	brain:	n/a	chr2:62713197-62713206
3	FOS	chr2:62713523-62713805	MCF10A-Er-Src	breast:	n/a	chr2:62713676-62713684 chr2:62713675-62713686
4	RXRA	chr2:62712891-62713536	HepG2	liver:	n/a	chr2:62713244-62713258

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62707580..62709394-chr2:62711860..62714496,2	MCF-7	breast:
2	chr2:62713307..62714054-chr2:62723005..62723908,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL18P	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11686597	0.97[ASN][1000 genomes]
rs11690138	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12988497	0.96[ASN][1000 genomes]
rs12989129	0.96[ASN][1000 genomes]
rs12993270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34282247	0.97[ASN][1000 genomes]
rs4608498	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs72805579	0.96[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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	22412388	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545946	TMEM17	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62703600-62724800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:62705800-62732200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:62706600-62726600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:62711400-62714600	Enhancers	Adipose Nuclei	Adipose
5	chr2:62712200-62713600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:62712200-62714600	Enhancers	Fetal Stomach	stomach
7	chr2:62712200-62714600	Enhancers	NHDF-Ad	bronchial
8	chr2:62712200-62715400	Enhancers	Ovary	ovary
9	chr2:62712400-62713800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:62712400-62714200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:62712600-62714000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:62712600-62714400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:62712600-62714600	Enhancers	Fetal Kidney	kidney
14	chr2:62712800-62713600	Enhancers	Aorta	Aorta
15	chr2:62712800-62713800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:62712800-62713800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr2:62712800-62714000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:62712800-62714000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:62712800-62714000	Enhancers	NHEK	skin
20	chr2:62712800-62714200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:62712800-62714400	Enhancers	HMEC	breast
22	chr2:62712800-62714600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:62712800-62714600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:62712800-62714600	Enhancers	Fetal Lung	lung
25	chr2:62712800-62714600	Enhancers	Fetal Muscle Leg	muscle
26	chr2:62712800-62714600	Enhancers	Pancreas	Pancrea
27	chr2:62713000-62713600	Enhancers	Liver	Liver
28	chr2:62713000-62713800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:62713000-62713800	Flanking Active TSS	A549	lung
30	chr2:62713000-62714000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:62713000-62714000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:62713000-62714000	Enhancers	Placenta	Placenta
33	chr2:62713000-62714200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:62713000-62714200	Enhancers	Colon Smooth Muscle	Colon
35	chr2:62713000-62714400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:62713000-62714400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:62713000-62714400	Enhancers	Fetal Heart	heart
38	chr2:62713000-62714600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:62713000-62714800	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:62713200-62713600	Enhancers	NH-A	brain
41	chr2:62713200-62713800	Enhancers	Brain Hippocampus Middle	brain
42	chr2:62713200-62713800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr2:62713200-62713800	Enhancers	NHLF	lung
44	chr2:62713200-62714000	Enhancers	Brain Anterior Caudate	brain
45	chr2:62713200-62714000	Enhancers	Esophagus	oesophagus
46	chr2:62713200-62714000	Enhancers	Lung	lung
47	chr2:62713200-62714000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:62713200-62714200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:62713200-62714200	Enhancers	Left Ventricle	heart
50	chr2:62713200-62714600	Enhancers	Fetal Thymus	thymus

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