Variant report

Variant	rs1961995
Chromosome Location	chr9:78993077-78993078
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:78992210..78995895-chr9:78999208..79002045,3	MCF-7	breast:
2	chr9:78991796..78994850-chr9:78999374..79004024,5	K562	blood:
3	chr9:78991603..78996204-chr9:79007851..79009683,4	MCF-7	breast:
4	chr9:78992990..78994682-chr9:79074040..79075808,2	MCF-7	breast:
5	chr9:78993024..78994920-chr9:79009980..79012177,2	MCF-7	breast:
6	chr9:78992647..78994850-chr9:78999374..79002879,3	K562	blood:
7	chr9:78991587..78996354-chr9:79007183..79010897,7	MCF-7	breast:
8	chr9:78991854..78994427-chr9:79006975..79009435,2	K562	blood:
9	chr8:117766615..117769384-chr9:78991570..78993615,2	MCF-7	breast:
10	chr9:78990957..78992471-chr9:78992875..78994908,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction
ENSG00000147677	Chromatin interaction
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10121699	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs10124695	0.92[ASN][1000 genomes]
rs10735646	0.82[CHB][hapmap]
rs10869767	0.84[ASN][1000 genomes]
rs10869773	0.81[ASN][1000 genomes]
rs11144864	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11144865	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11144871	0.84[ASN][1000 genomes]
rs11144880	0.82[ASN][1000 genomes]
rs11788095	0.91[ASN][1000 genomes]
rs12057052	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13288968	0.96[ASN][1000 genomes]
rs13295433	0.81[ASN][1000 genomes]
rs13302654	0.86[ASN][1000 genomes]
rs1535845	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2002423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251604	0.84[ASN][1000 genomes]
rs2377639	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2490572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2490573	0.86[ASN][1000 genomes]
rs2490574	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490576	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490579	0.84[ASN][1000 genomes]
rs2490583	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2490584	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2490586	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2501920	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2501922	0.83[ASN][1000 genomes]
rs2501923	0.84[ASN][1000 genomes]
rs2501925	0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2501927	0.84[ASN][1000 genomes]
rs2501928	0.88[ASN][1000 genomes]
rs2501930	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2501932	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501933	0.86[ASN][1000 genomes]
rs2501935	0.86[ASN][1000 genomes]
rs2501937	0.94[ASN][1000 genomes]
rs2501938	0.94[ASN][1000 genomes]
rs2501939	0.95[ASN][1000 genomes]
rs2501940	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501942	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3739729	0.84[ASN][1000 genomes]
rs4372070	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4745541	0.83[ASN][1000 genomes]
rs4745544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4745545	0.88[ASN][1000 genomes]
rs4745546	0.87[ASN][1000 genomes]
rs6560517	0.81[ASN][1000 genomes]
rs6560522	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs7847608	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7849239	0.81[ASN][1000 genomes]
rs7861089	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1961995	RFK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78984600-78993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:78988200-78993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
7	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
9	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
11	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:78988600-78994200	Weak transcription	HMEC	breast
14	chr9:78988600-79001000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:78988600-79001000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:78988600-79002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:78988800-78999800	Weak transcription	Brain Anterior Caudate	brain
20	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
21	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:78989000-78998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:78989000-78999800	Weak transcription	GM12878-XiMat	blood
25	chr9:78989000-79000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:78989000-79000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:78989200-78997800	Weak transcription	Ovary	ovary
28	chr9:78989800-78995000	Weak transcription	Gastric	stomach
29	chr9:78989800-78999800	Weak transcription	Aorta	Aorta
30	chr9:78990000-78998600	Weak transcription	Colonic Mucosa	Colon
31	chr9:78990000-79005400	Weak transcription	Small Intestine	intestine
32	chr9:78990200-78999000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
34	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
35	chr9:78990400-78993800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:78990400-78994400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:78990400-78994600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:78990400-78994600	Weak transcription	Pancreas	Pancrea
39	chr9:78990400-78998400	Weak transcription	Adipose Nuclei	Adipose
40	chr9:78990400-78998800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:78990400-78999000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:78990400-78999200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:78990400-78999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:78990400-78999200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:78990400-78999600	Weak transcription	Left Ventricle	heart
46	chr9:78990400-78999600	Weak transcription	HSMM	muscle
47	chr9:78990400-78999800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:78990400-78999800	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:78990400-79001000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:78990400-79002600	Weak transcription	Esophagus	oesophagus

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