Variant report

Variant	rs12630070
Chromosome Location	chr3:195990822-195990823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195988880..195993389-chr3:196013030..196017902,6	MCF-7	breast:
2	chr3:195977668..195980618-chr3:195990006..195991667,2	MCF-7	breast:
3	chr3:195989073..195991796-chr3:195994063..195996834,4	K562	blood:
4	chr3:195987889..195991350-chr3:195994108..195996834,3	K562	blood:
5	chr3:195990043..195995606-chr3:196012923..196017600,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1045075	0.80[MEX][hapmap]
rs11185520	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491227	0.84[MEX][hapmap]
rs12637288	0.85[JPT][hapmap]
rs1476331	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs17852687	0.84[MEX][hapmap]
rs1948690	0.82[JPT][hapmap]
rs2047551	0.85[JPT][hapmap]
rs2088666	0.85[JPT][hapmap]
rs2280526	0.84[CHD][hapmap]
rs3772109	0.88[ASW][hapmap];0.85[JPT][hapmap]
rs4916421	0.85[JPT][hapmap]
rs59815219	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60680644	0.90[ASN][1000 genomes]
rs67723323	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777819	0.84[CHD][hapmap]
rs73212143	0.87[ASN][1000 genomes]
rs7625886	0.83[JPT][hapmap]
rs7631913	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs7636149	0.88[ASW][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs7639752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9343	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs939883	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription 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	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic 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	49 gene(s)	inside rSNPs	diseases
13	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
18	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats 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	64 gene(s)	inside rSNPs	diseases
20	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12630070	SLC51A	cis	Heart Left Ventricle	GTEx
rs12630070	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs12630070	SLC51A	cis	Esophagus Muscularis	GTEx
rs12630070	SLC51A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965200-195994200	Weak transcription	A549	lung
2	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:195968800-195993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
5	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
6	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
10	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
11	chr3:195975000-195994000	Weak transcription	Right Ventricle	heart
12	chr3:195975000-195995000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:195975000-195997200	Weak transcription	Esophagus	oesophagus
14	chr3:195975000-195999600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:195975200-195991200	Weak transcription	Thymus	Thymus
16	chr3:195975200-195992800	Weak transcription	Brain Anterior Caudate	brain
17	chr3:195975200-195993400	Weak transcription	Aorta	Aorta
18	chr3:195975200-195994200	Weak transcription	Fetal Kidney	kidney
19	chr3:195975200-195994200	Weak transcription	Gastric	stomach
20	chr3:195975400-195992400	Weak transcription	Lung	lung
21	chr3:195975400-195993400	Weak transcription	Colonic Mucosa	Colon
22	chr3:195976400-195994200	Weak transcription	Spleen	Spleen
23	chr3:195978200-195994800	Weak transcription	Brain Angular Gyrus	brain
24	chr3:195978400-195994200	Weak transcription	Brain Substantia Nigra	brain
25	chr3:195978800-195994200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:195979000-195993400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:195979000-195995000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:195981200-195995200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:195981400-195994600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:195981400-195997800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:195982200-195994200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:195982400-195997600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:195982800-195995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:195983000-195995800	Weak transcription	HMEC	breast
35	chr3:195983200-195999800	Weak transcription	Psoas Muscle	Psoas
36	chr3:195983600-195993400	Weak transcription	Ovary	ovary
37	chr3:195983800-195991400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:195984000-195997400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:195984200-195991200	Weak transcription	Brain Germinal Matrix	brain
40	chr3:195984200-195994000	Weak transcription	Hela-S3	cervix
41	chr3:195984400-195994200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:195984800-195991200	Weak transcription	Left Ventricle	heart
43	chr3:195984800-195991400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:195984800-195992400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:195984800-195994200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:195984800-196005000	Weak transcription	Fetal Heart	heart
47	chr3:195985000-195992400	Weak transcription	Dnd41	blood
48	chr3:195985000-195994000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:195985800-195991200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:195987000-195995200	Strong transcription	Primary monocytes fromperipheralblood	blood

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