Variant report

Variant	rs7729984
Chromosome Location	chr5:179697535-179697536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179682736..179685414-chr5:179695903..179698661,2	MCF-7	breast:
2	chr5:179693858..179696723-chr5:179696767..179698335,2	K562	blood:
3	chr5:179695931..179698404-chr5:179718906..179720620,2	K562	blood:
4	chr5:179683794..179686507-chr5:179697263..179699812,2	K562	blood:
5	chr5:179696724..179698637-chr5:179701872..179704332,2	K562	blood:
6	chr5:179692679..179694795-chr5:179697303..179699548,2	K562	blood:
7	chr5:179697473..179700206-chr5:179706541..179709414,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000253908	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000248367	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3812067	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs6601105	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601106	0.96[EUR][1000 genomes]
rs6872544	0.95[EUR][1000 genomes]
rs9968653	0.96[CEU][hapmap];0.97[EUR][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	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7729984	RASGEF1C	cis	brain	BrainEAC

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
3	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
4	chr5:179660800-179706800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:179673600-179701800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr5:179673600-179705400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:179677000-179703000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:179681800-179705600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:179691200-179706200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:179692800-179705000	Weak transcription	Stomach Mucosa	stomach
12	chr5:179692800-179718000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:179693800-179697600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:179693800-179709600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:179694000-179699000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:179694000-179699400	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:179694200-179699000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:179694200-179701400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:179694200-179702200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:179694200-179702400	Weak transcription	Brain Angular Gyrus	brain
21	chr5:179694200-179702800	Weak transcription	Hela-S3	cervix
22	chr5:179694400-179699000	Weak transcription	NHDF-Ad	bronchial
23	chr5:179694400-179701400	Weak transcription	Brain Germinal Matrix	brain
24	chr5:179694800-179697600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:179694800-179698000	Weak transcription	HSMM	muscle
26	chr5:179694800-179717600	Weak transcription	HUVEC	blood vessel
27	chr5:179695200-179697600	Weak transcription	Aorta	Aorta
28	chr5:179695200-179700800	Weak transcription	Fetal Thymus	thymus
29	chr5:179695400-179698600	Weak transcription	Osteobl	bone
30	chr5:179695400-179699200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:179695400-179702200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:179695400-179704200	Weak transcription	HepG2	liver
33	chr5:179695600-179698200	Weak transcription	K562	blood
34	chr5:179695600-179699000	Weak transcription	Fetal Kidney	kidney
35	chr5:179695600-179699000	Weak transcription	Pancreas	Pancrea
36	chr5:179695600-179704200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:179695800-179699400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:179695800-179699800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:179695800-179706200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:179696200-179697600	Weak transcription	Gastric	stomach
41	chr5:179696200-179699000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:179696200-179699000	Weak transcription	Left Ventricle	heart
43	chr5:179696200-179699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:179696200-179699800	Weak transcription	Right Ventricle	heart
45	chr5:179696200-179701400	Weak transcription	Fetal Stomach	stomach
46	chr5:179696200-179704200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:179696400-179698000	Weak transcription	HSMMtube	muscle
48	chr5:179696400-179698200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:179696400-179698400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:179696400-179698400	Weak transcription	Fetal Intestine Large	intestine

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