Variant report

Variant	rs12636232
Chromosome Location	chr3:50157895-50157896
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50157801..50161419-chr3:50224013..50228566,6	MCF-7	breast:
2	chr3:50157579..50160318-chr3:50233509..50235124,2	MCF-7	breast:
3	chr3:50157617..50159229-chr3:50261958..50264421,2	MCF-7	breast:
4	chr3:50157890..50164898-chr3:50186493..50191745,15	MCF-7	breast:
5	chr3:50157879..50160528-chr3:50162974..50166130,4	K562	blood:
6	chr3:50153410..50155870-chr3:50157177..50159023,3	K562	blood:
7	chr3:50156913..50158492-chr3:50221059..50222752,2	K562	blood:
8	chr3:50157123..50160509-chr3:50182287..50185771,3	MCF-7	breast:
9	chr3:50157840..50167526-chr3:50182100..50196634,43	MCF-7	breast:
10	chr3:50157403..50159553-chr3:50273403..50275024,2	K562	blood:
11	chr3:50131320..50133089-chr3:50157321..50159844,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000001617	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000235016	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11130230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11130237	1.00[ASW][hapmap];1.00[CEU][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11130239	0.86[GIH][hapmap];0.86[TSI][hapmap]
rs11130240	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11916261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919418	1.00[JPT][hapmap]
rs11920034	1.00[ASW][hapmap];1.00[CEU][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928995	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486470	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486808	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12490944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12492291	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494077	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494172	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494916	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495114	1.00[ASW][hapmap];1.00[CEU][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12629677	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12631192	1.00[JPT][hapmap]
rs12631248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs12631309	0.89[AMR][1000 genomes]
rs12632751	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636045	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636449	0.90[EUR][1000 genomes]
rs12636669	0.89[AMR][1000 genomes]
rs12637222	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12637457	1.00[ASW][hapmap];1.00[CEU][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12638046	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12639175	1.00[JPT][hapmap]
rs13100903	0.94[ASN][1000 genomes]
rs2003485	0.87[ASN][1000 genomes]
rs2023951	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023952	1.00[ASW][hapmap];1.00[CEU][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188151	1.00[JPT][hapmap]
rs2518796	1.00[JPT][hapmap]
rs35333166	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57009357	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs59802870	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60429865	0.84[EUR][1000 genomes]
rs61491513	0.89[AMR][1000 genomes]
rs61729114	0.89[AMR][1000 genomes]
rs62260770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260771	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260773	0.86[EUR][1000 genomes]
rs62262096	0.89[AMR][1000 genomes]
rs62262099	0.89[AMR][1000 genomes]
rs62262104	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262116	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262138	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262144	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62263578	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62263580	0.81[EUR][1000 genomes]
rs62263584	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263586	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263588	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263590	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263591	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263597	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62263600	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv818139	chr3:50144951-50174572	Weak transcription Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
8	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
11	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
12	esv3386929	chr3:50156348-50161346	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
14	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12636232	MON1A	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50128000-50158000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:50128000-50158000	Strong transcription	Fetal Muscle Trunk	muscle
3	chr3:50128200-50158800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:50128400-50158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:50128400-50158400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:50128400-50159000	Strong transcription	Lung	lung
7	chr3:50128600-50158000	Strong transcription	NH-A	brain
8	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
12	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
14	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
16	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
17	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:50128600-50159200	Strong transcription	Liver	Liver
20	chr3:50128600-50159200	Strong transcription	NHEK	skin
21	chr3:50128600-50160400	Strong transcription	Fetal Thymus	thymus
22	chr3:50128800-50158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:50128800-50158600	Strong transcription	HMEC	breast
24	chr3:50128800-50159000	Strong transcription	Brain Anterior Caudate	brain
25	chr3:50129000-50158600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:50129000-50158600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:50129000-50158800	Strong transcription	Fetal Intestine Large	intestine
28	chr3:50129000-50159000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:50129000-50159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:50129000-50159200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:50129000-50159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:50129000-50159400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:50129000-50160000	Strong transcription	Fetal Stomach	stomach
34	chr3:50129000-50160000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:50129000-50160800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:50129200-50158600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr3:50129200-50158800	Strong transcription	Primary B cells from cord blood	blood
38	chr3:50129200-50158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:50129200-50158800	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:50129200-50159000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:50129200-50159600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:50129200-50160000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:50129200-50160200	Strong transcription	Fetal Brain Female	brain
44	chr3:50129400-50158800	Strong transcription	Pancreas	Pancrea
45	chr3:50129400-50159400	Strong transcription	Spleen	Spleen
46	chr3:50129600-50159200	Strong transcription	Primary T cells from cord blood	blood
47	chr3:50129600-50161600	Strong transcription	Thymus	Thymus
48	chr3:50129800-50158400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:50129800-50158400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:50129800-50158600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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