Variant report

Variant	rs2672215
Chromosome Location	chr11:3691649-3691650
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:3691626-3692244	K562	blood:	n/a	n/a
2	POLR2A	chr11:3690470-3692477	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr11:3691620-3691709	K562	blood:	n/a	n/a
4	POLR2A	chr11:3689767-3694248	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr11:3690963-3694280	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3690214..3692780-chr11:3696076..3698742,2	MCF-7	breast:
2	chr11:3690371..3694787-chr11:3695669..3699766,6	K562	blood:

Variant related genes	Relation type
CHRNA10	TF binding region
ENSG00000110713	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10767513	0.80[EUR][1000 genomes]
rs11029018	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11029026	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12362156	0.96[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2231532	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2672216	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2672217	0.92[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2741863	0.91[JPT][hapmap]
rs2741865	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2741866	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs276900	0.81[JPT][hapmap]
rs4261313	0.96[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4600243	0.82[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4910976	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs623056	0.82[JPT][hapmap]
rs6578413	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs683142	0.84[EUR][1000 genomes]
rs694164	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047763	chr11:2918998-3751029	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	esv2758252	chr11:3236512-3801429	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2759796	chr11:3236512-3801429	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv832051	chr11:3523947-3728714	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1820972	chr11:3616884-3801429	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv1821329	chr11:3616884-3801429	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv832052	chr11:3616884-3801429	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
8	nsv428247	chr11:3616884-3801429	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv526441	chr11:3626177-3756686	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1046356	chr11:3628837-3774215	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv1044345	chr11:3628912-3739222	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv540906	chr11:3628912-3739222	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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 target site	11 gene(s)	inside rSNPs	diseases
13	nsv1044419	chr11:3628912-3751029	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
15	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
16	nsv1043716	chr11:3685149-3751029	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
17	nsv540908	chr11:3685149-3751029	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv482156	chr11:3686817-3692614	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2672215	RRM1	cis	cerebellum	SCAN
rs2672215	UBQLNL	cis	parietal	SCAN
rs2672215	INS-IGF2	cis	parietal	SCAN
rs2672215	TMEM80	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3681800-3693200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:3682400-3697200	Weak transcription	Fetal Brain Male	brain
3	chr11:3683000-3696600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:3683200-3694000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:3683600-3693400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:3683600-3693400	Weak transcription	NHDF-Ad	bronchial
7	chr11:3684400-3705400	Strong transcription	Fetal Muscle Leg	muscle
8	chr11:3685000-3693200	Weak transcription	Hela-S3	cervix
9	chr11:3685000-3728000	Strong transcription	Stomach Smooth Muscle	stomach
10	chr11:3685000-3743800	Strong transcription	Duodenum Mucosa	Duodenum
11	chr11:3685200-3691800	Strong transcription	Ovary	ovary
12	chr11:3685200-3693200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:3685200-3695400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:3685200-3702600	Strong transcription	Fetal Intestine Small	intestine
15	chr11:3685200-3705600	Strong transcription	Brain Germinal Matrix	brain
16	chr11:3685200-3728200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:3685200-3728200	Strong transcription	Thymus	Thymus
18	chr11:3685200-3730000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:3685200-3766800	Strong transcription	Placenta	Placenta
20	chr11:3685400-3694600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:3685400-3694600	Strong transcription	Gastric	stomach
22	chr11:3685400-3695200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:3685400-3704800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:3685400-3704800	Strong transcription	Brain Hippocampus Middle	brain
25	chr11:3685400-3705200	Strong transcription	Spleen	Spleen
26	chr11:3685400-3705400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:3685400-3711000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:3685400-3728200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:3685400-3728400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:3685400-3731200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:3685400-3733400	Strong transcription	Fetal Intestine Large	intestine
32	chr11:3685400-3739000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:3685400-3741600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:3685400-3743800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:3685400-3802600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:3685600-3694000	Strong transcription	Aorta	Aorta
37	chr11:3685600-3698000	Strong transcription	Esophagus	oesophagus
38	chr11:3685600-3719000	Strong transcription	Primary T cells from cord blood	blood
39	chr11:3685600-3728400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:3685600-3728400	Strong transcription	Adipose Nuclei	Adipose
41	chr11:3685600-3805600	Strong transcription	Fetal Thymus	thymus
42	chr11:3685800-3695800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:3685800-3710800	Strong transcription	Brain Anterior Caudate	brain
44	chr11:3685800-3754200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:3685800-3776200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr11:3685800-3779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:3686000-3698200	Strong transcription	Fetal Brain Female	brain
48	chr11:3686000-3779800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:3686200-3693800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr11:3686400-3693600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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