Variant report

Variant	rs1147702
Chromosome Location	chr3:120126377-120126378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1147704	0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1147705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708297	0.80[ASN][1000 genomes]
rs11713799	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11718087	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1259290	0.85[CHD][hapmap]
rs1259291	0.92[ASN][1000 genomes]
rs1259292	0.92[ASN][1000 genomes]
rs1259293	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1259294	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1259295	1.00[JPT][hapmap]
rs1259296	0.92[ASN][1000 genomes]
rs1259297	0.81[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1259307	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259327	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1356112	0.81[ASN][1000 genomes]
rs1588890	0.82[CHB][hapmap]
rs1606871	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1617553	0.81[ASN][1000 genomes]
rs16831067	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16831087	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1716838	0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs1716839	0.81[ASN][1000 genomes]
rs1733324	0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs1733329	0.92[CHD][hapmap]
rs2091727	0.81[ASN][1000 genomes]
rs2673701	0.81[ASN][1000 genomes]
rs2673704	0.81[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2700260	0.93[JPT][hapmap]
rs2700261	0.87[ASN][1000 genomes]
rs2702158	0.92[CHD][hapmap]
rs2943754	0.92[CHD][hapmap]
rs6438578	0.82[CHD][hapmap]
rs7616519	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7616807	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs916509	0.87[JPT][hapmap]
rs916510	0.90[ASN][1000 genomes]
rs916511	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs916512	0.87[JPT][hapmap]
rs939500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1147702	C3orf1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120112000-120132600	Strong transcription	Placenta Amnion	Placenta Amnion
2	chr3:120112200-120127400	Strong transcription	Left Ventricle	heart
3	chr3:120112200-120130000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr3:120112200-120131400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:120112200-120132600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:120112400-120129600	Strong transcription	Stomach Smooth Muscle	stomach
7	chr3:120112400-120130200	Strong transcription	Adipose Nuclei	Adipose
8	chr3:120112400-120132600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:120112400-120132600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:120112400-120132600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:120112400-120132600	Strong transcription	HSMMtube	muscle
12	chr3:120112400-120132600	Strong transcription	NH-A	brain
13	chr3:120112400-120132600	Strong transcription	NHDF-Ad	bronchial
14	chr3:120112400-120132600	Strong transcription	NHLF	lung
15	chr3:120112600-120130600	Strong transcription	Ovary	ovary
16	chr3:120112600-120131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:120112600-120132400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:120112600-120132400	Strong transcription	Aorta	Aorta
19	chr3:120112600-120132600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:120112600-120132600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:120112600-120132800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:120112800-120131200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:120112800-120132000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:120112800-120132600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:120112800-120132600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:120113200-120127400	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:120113200-120132400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:120113200-120132600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:120113200-120132600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:120113200-120132600	Strong transcription	Fetal Kidney	kidney
31	chr3:120113200-120132600	Strong transcription	HUVEC	blood vessel
32	chr3:120113200-120133000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:120113400-120126400	Strong transcription	Right Ventricle	heart
34	chr3:120113400-120126800	Strong transcription	Placenta	Placenta
35	chr3:120113400-120132400	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr3:120113400-120132600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:120113400-120132600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:120113800-120132600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:120114000-120132400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:120114200-120129600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:120114400-120132600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:120114400-120132800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
44	chr3:120114600-120128000	Strong transcription	Fetal Stomach	stomach
45	chr3:120114800-120128800	Strong transcription	Fetal Lung	lung
46	chr3:120114800-120128800	Strong transcription	NHEK	skin
47	chr3:120114800-120129200	Strong transcription	Colon Smooth Muscle	Colon
48	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:120116400-120126400	Weak transcription	Brain Substantia Nigra	brain
50	chr3:120117600-120128200	Weak transcription	Brain Hippocampus Middle	brain

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