Variant report

Variant	rs12028967
Chromosome Location	chr1:113489770-113489771
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113488767..113491029-chr1:113497623..113499178,2	MCF-7	breast:
2	chr1:113476694..113481534-chr1:113488143..113494233,11	K562	blood:
3	chr1:113485184..113487330-chr1:113488686..113492213,4	K562	blood:

Variant related genes	Relation type
ENSG00000155380	Chromatin interaction
ENSG00000226419	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10399593	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1049434	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10776763	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857980	0.83[YRI][hapmap]
rs10857981	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10857982	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857983	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11102559	0.86[EUR][1000 genomes]
rs11102562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102565	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102568	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12037621	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12043035	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1344429	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1539625	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1629027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17030905	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs2002402	0.86[EUR][1000 genomes]
rs2360009	0.86[EUR][1000 genomes]
rs3789592	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs3889656	0.82[CEU][hapmap]
rs4301628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839273	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57549167	0.89[EUR][1000 genomes]
rs61819971	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61819997	0.89[EUR][1000 genomes]
rs6537764	0.86[ASN][1000 genomes]
rs6537765	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6663872	0.92[ASN][1000 genomes]
rs6682142	0.94[EUR][1000 genomes]
rs7169	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7551223	0.89[ASN][1000 genomes]
rs7556664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9787311	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12028967	LRIG2	cis	parietal	SCAN
rs12028967	DENND2C	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113458000-113490600	Weak transcription	Right Atrium	heart
2	chr1:113466400-113496400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:113467000-113493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:113467000-113495600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:113467000-113497400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:113467200-113496400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:113468000-113496200	Weak transcription	Fetal Brain Female	brain
8	chr1:113468200-113495400	Weak transcription	Psoas Muscle	Psoas
9	chr1:113469800-113495600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:113469800-113495600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:113469800-113497000	Weak transcription	Fetal Stomach	stomach
12	chr1:113471800-113493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:113473000-113495000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:113473000-113495400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:113478800-113493200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:113481000-113493000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:113481000-113493000	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:113481000-113495600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:113481000-113495600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:113481000-113496200	Weak transcription	Brain Angular Gyrus	brain
21	chr1:113481000-113496200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:113481000-113496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:113481200-113489800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:113481200-113492800	Weak transcription	HepG2	liver
25	chr1:113481200-113493200	Weak transcription	Right Ventricle	heart
26	chr1:113481200-113493800	Weak transcription	HUVEC	blood vessel
27	chr1:113481200-113495400	Weak transcription	Liver	Liver
28	chr1:113481200-113495600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:113481200-113496200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:113481200-113496200	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:113481200-113496200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:113481200-113496200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:113481200-113496400	Weak transcription	A549	lung
34	chr1:113481400-113495200	Weak transcription	HMEC	breast
35	chr1:113481400-113495400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:113481400-113496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:113481400-113496200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:113481400-113496200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:113481400-113497000	Weak transcription	Osteobl	bone
40	chr1:113483200-113492800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:113484200-113496200	Weak transcription	HSMMtube	muscle
42	chr1:113484400-113490400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:113484800-113492600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:113485000-113493200	Weak transcription	Left Ventricle	heart
45	chr1:113485400-113490000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:113486000-113492800	Weak transcription	Dnd41	blood
47	chr1:113486000-113494600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:113486000-113495000	Weak transcription	HSMM	muscle
49	chr1:113487000-113493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:113487400-113492000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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