Variant report

Variant	rs3800939
Chromosome Location	chr7:102574715-102574716
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	CTBP2	chr7:102574261-102574739	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr7:102573826-102574908	IMR90	lung:	n/a	n/a
3	TCF12	chr7:102573943-102574765	SK-N-SH	brain:	n/a	chr7:102574344-102574351 chr7:102574342-102574352
4	CREB1	chr7:102573806-102574776	H1-hESC	embryonic stem cell:	n/a	n/a
5	RCOR1	chr7:102573606-102574974	IMR90	lung:	n/a	n/a
6	EP300	chr7:102573385-102577692	SK-N-SH	brain:	n/a	n/a
7	MAZ	chr7:102573830-102574722	IMR90	lung:	n/a	n/a
8	MXI1	chr7:102574041-102575611	IMR90	lung:	n/a	n/a
9	CREB1	chr7:102574184-102574742	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LRRC17	TF binding region
FBXL13	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11543780	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs12668311	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12670723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12673840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17136122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28817087	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3748110	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4457269	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59099783	0.90[AMR][1000 genomes]
rs60545001	1.00[AFR][1000 genomes]
rs61749912	0.81[AMR][1000 genomes]
rs6465884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6465890	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6942688	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6963884	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs6969209	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7798381	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800939	ZNF117	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102568600-102574800	Weak transcription	Osteobl	bone
3	chr7:102571400-102579600	Genic enhancers	HSMM	muscle
4	chr7:102571600-102574800	Weak transcription	Aorta	Aorta
5	chr7:102571600-102581800	Weak transcription	Fetal Intestine Small	intestine
6	chr7:102571800-102579400	Weak transcription	Left Ventricle	heart
7	chr7:102573000-102576800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:102573000-102576800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:102573000-102577600	Genic enhancers	Fetal Stomach	stomach
10	chr7:102573200-102576200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:102573200-102577000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr7:102573200-102578200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:102573400-102575400	Genic enhancers	NH-A	brain
14	chr7:102573400-102575600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:102573400-102575600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:102573400-102575600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:102573400-102576800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:102573400-102578600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:102573400-102579400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:102573400-102579800	Genic enhancers	Fetal Lung	lung
21	chr7:102573600-102574800	Enhancers	Fetal Muscle Leg	muscle
22	chr7:102573600-102575600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:102573600-102575600	Enhancers	Fetal Thymus	thymus
24	chr7:102573600-102577400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:102573800-102574800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
26	chr7:102573800-102574800	Enhancers	Brain Substantia Nigra	brain
27	chr7:102573800-102575600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr7:102573800-102577200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr7:102573800-102591400	Weak transcription	Pancreas	Pancrea
30	chr7:102574000-102574800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:102574000-102574800	Enhancers	Fetal Brain Female	brain
32	chr7:102574000-102574800	Weak transcription	NHLF	lung
33	chr7:102574000-102575000	Flanking Active TSS	HSMMtube	muscle
34	chr7:102574000-102575200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr7:102574000-102575600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr7:102574000-102575600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:102574000-102575600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:102574000-102575600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:102574000-102575600	Enhancers	Stomach Mucosa	stomach
40	chr7:102574000-102592200	Weak transcription	Fetal Intestine Large	intestine
41	chr7:102574200-102574800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:102574200-102574800	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr7:102574200-102575600	Enhancers	Brain Hippocampus Middle	brain
44	chr7:102574200-102576800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:102574200-102579600	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:102574400-102574800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
47	chr7:102574400-102574800	Strong transcription	K562	blood
48	chr7:102574400-102575000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr7:102574400-102575600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr7:102574400-102575600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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