Variant report

Variant	rs2712158
Chromosome Location	chr4:48857387-48857388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48781641..48784567-chr4:48855819..48858602,2	MCF-7	breast:
2	chr4:48831337..48833457-chr4:48856864..48859835,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11727343	0.89[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11729065	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11733534	0.86[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734191	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11939889	0.83[EUR][1000 genomes]
rs11943219	0.83[EUR][1000 genomes]
rs12504699	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12512637	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12641022	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13109500	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13119414	0.84[EUR][1000 genomes]
rs13141523	0.84[CEU][hapmap]
rs13141838	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13149083	0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs13152270	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1463365	0.81[ASN][1000 genomes]
rs1463367	0.80[MEX][hapmap]
rs16861510	0.83[YRI][hapmap]
rs1980193	0.84[EUR][1000 genomes]
rs2085292	0.84[CHD][hapmap]
rs2176460	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2289065	0.80[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2290516	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2354938	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2572345	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572350	0.91[ASW][hapmap];0.92[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712156	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712157	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883562	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34730980	0.80[ASN][1000 genomes]
rs3761729	0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4694904	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4694906	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695400	0.83[EUR][1000 genomes]
rs4695401	0.83[EUR][1000 genomes]
rs4695407	0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57797824	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62310934	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6447655	0.81[EUR][1000 genomes]
rs6447666	0.88[GIH][hapmap]
rs6830078	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6830848	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7654032	0.88[ASN][1000 genomes]
rs7657332	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs7657698	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7665209	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7680280	0.81[EUR][1000 genomes]
rs7681070	0.81[EUR][1000 genomes]
rs7687992	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7697522	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9291326	0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637562	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9790336	0.81[EUR][1000 genomes]
rs9997920	0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2712158	MGC45416	cis	multi-tissue	Pritchard
rs2712158	SLC10A4	cis	lung	GTEx
rs2712158	OCIAD2	cis	cerebellum	SCAN
rs2712158	OCIAD1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48834000-48859800	Weak transcription	Aorta	Aorta
2	chr4:48834000-48864600	Weak transcription	Stomach Mucosa	stomach
3	chr4:48835000-48858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:48835000-48859800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:48835000-48861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:48835000-48862400	Strong transcription	Fetal Thymus	thymus
7	chr4:48835000-48863000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:48835000-48864400	Strong transcription	HSMM	muscle
9	chr4:48835200-48863200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:48835200-48863800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:48835200-48864200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:48835400-48857400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:48835400-48863200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:48835400-48863400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:48835600-48864000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:48835800-48863200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:48836000-48858000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:48836000-48863600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:48836200-48863600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:48836800-48863200	Strong transcription	Dnd41	blood
21	chr4:48837200-48861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:48838000-48859600	Weak transcription	Gastric	stomach
23	chr4:48838000-48859600	Weak transcription	Spleen	Spleen
24	chr4:48838000-48859800	Weak transcription	Pancreas	Pancrea
25	chr4:48838000-48859800	Weak transcription	Right Ventricle	heart
26	chr4:48838000-48864400	Weak transcription	Esophagus	oesophagus
27	chr4:48838200-48866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:48838400-48863400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:48839400-48859600	Weak transcription	Colonic Mucosa	Colon
30	chr4:48840200-48860000	Weak transcription	Small Intestine	intestine
31	chr4:48841000-48865400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:48844200-48857400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr4:48844800-48858000	Strong transcription	Liver	Liver
34	chr4:48845400-48863800	Weak transcription	Hela-S3	cervix
35	chr4:48848200-48864600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:48848200-48864600	Weak transcription	Fetal Heart	heart
37	chr4:48848200-48880000	Weak transcription	Brain Substantia Nigra	brain
38	chr4:48849800-48858200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:48850800-48857800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:48851200-48860800	Strong transcription	Placenta	Placenta
41	chr4:48852000-48858000	Strong transcription	Left Ventricle	heart
42	chr4:48852000-48861800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:48852000-48863600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr4:48852000-48863800	Strong transcription	Fetal Intestine Large	intestine
45	chr4:48852800-48859800	Weak transcription	Lung	lung
46	chr4:48852800-48859800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:48852800-48860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:48853000-48858000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:48853000-48859600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:48853200-48858200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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