Variant report

Variant	rs9329096
Chromosome Location	chr5:179479621-179479622
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179232497..179234437-chr5:179477611..179480495,2	K562	blood:
2	chr5:179478110..179479626-chr5:179490709..179493377,2	K562	blood:
3	chr5:179477454..179480172-chr5:179480653..179484113,3	MCF-7	breast:
4	chr5:179279889..179282788-chr5:179478192..179480009,2	K562	blood:
5	chr5:179473631..179475664-chr5:179477740..179480217,2	K562	blood:
6	chr5:179474524..179477374-chr5:179479073..179481485,2	MCF-7	breast:
7	chr5:179474733..179479669-chr5:179495487..179500173,5	K562	blood:

Variant related genes	Relation type
ENSG00000161011	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000161013	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10036834	0.81[CEU][hapmap]
rs10051632	0.81[EUR][1000 genomes]
rs10061480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10068039	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10068529	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10068594	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10078977	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10464097	0.81[EUR][1000 genomes]
rs10479455	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10479557	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10903246	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1102190	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1103811	0.81[GIH][hapmap]
rs12153541	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12653944	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12656219	0.83[CHB][hapmap];0.98[CHD][hapmap];0.82[ASN][1000 genomes]
rs173562	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs185076	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs193718	0.89[CHD][hapmap]
rs2386704	0.83[ASN][1000 genomes]
rs248257	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs248258	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs248316	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs248319	0.85[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs27013	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs27014	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27016	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27017	0.89[CHD][hapmap]
rs27019	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs394588	0.81[EUR][1000 genomes]
rs4130025	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs418384	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4340879	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4466125	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs449511	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4700855	0.83[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4700858	0.88[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap]
rs55734821	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62405020	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62405021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6871596	0.81[EUR][1000 genomes]
rs6884290	0.88[ASN][1000 genomes]
rs6888883	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7706570	0.96[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7734329	0.84[LWK][hapmap]
rs857182	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs857183	0.86[EUR][1000 genomes]
rs857189	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	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
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	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
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9329096	RASGEF1C	cis	parietal	SCAN
rs9329096	TRIM7	cis	parietal	SCAN
rs9329096	RASGEF1C	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
6	chr5:179467400-179483200	Weak transcription	HSMM	muscle
7	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
8	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
9	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
10	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
12	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:179475200-179481600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr5:179475800-179483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:179476000-179481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:179476000-179484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:179476000-179497800	Weak transcription	Lung	lung
19	chr5:179476400-179481400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:179476400-179486200	Weak transcription	Ovary	ovary
21	chr5:179476400-179487000	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
23	chr5:179476800-179480200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:179477200-179480000	Weak transcription	Fetal Lung	lung
25	chr5:179477400-179480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:179477400-179480200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:179477400-179481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:179477400-179483800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:179477400-179495000	Weak transcription	Gastric	stomach
31	chr5:179477600-179479800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:179477600-179480200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:179477600-179483600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:179477600-179486200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:179477800-179480000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:179477800-179480000	Weak transcription	Liver	Liver
37	chr5:179477800-179481400	Weak transcription	HepG2	liver
38	chr5:179478000-179480000	Weak transcription	Adipose Nuclei	Adipose
39	chr5:179478000-179480000	Weak transcription	Pancreas	Pancrea
40	chr5:179478000-179480200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:179478000-179482400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
43	chr5:179478200-179480400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:179478200-179481200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:179478200-179481200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:179478400-179484200	Enhancers	Brain Hippocampus Middle	brain
47	chr5:179478600-179480400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:179478600-179480600	Enhancers	Brain Angular Gyrus	brain
49	chr5:179478600-179481400	Enhancers	Brain Germinal Matrix	brain
50	chr5:179478800-179480200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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