Variant report

Variant	rs2278563
Chromosome Location	chr2:97212693-97212694
allele	C/T
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	chr2:97211812-97213379	GM18505	blood:	n/a	n/a
2	POLR2A	chr2:97211684-97213333	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:97211377-97213751	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:97211545-97214013	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:97211710-97213387	GM12892	blood:	n/a	n/a
6	RUNX3	chr2:97212503-97212851	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:97211862-97213329	GM19193	blood:	n/a	n/a
8	POLR2A	chr2:97211604-97213964	GM12892	blood:	n/a	n/a
9	ZNF263	chr2:97212685-97213299	HEK293-T-REx	kidney:	n/a	chr2:97212815-97212824 chr2:97213095-97213116
10	POLR2A	chr2:97211544-97213984	GM12892	blood:	n/a	n/a
11	POLR2A	chr2:97212022-97213399	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:97211722-97213932	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:97211811-97213923	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:97211682-97213013	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:97211632-97213870	GM12891	blood:	n/a	n/a
16	POLR2A	chr2:97211619-97213909	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:97211795-97213825	GM12891	blood:	n/a	n/a
18	POLR2A	chr2:97211004-97213891	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97210607..97212874-chr2:97219219..97220730,2	K562	blood:

Variant related genes	Relation type
ARID5A	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10460601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164109	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11677722	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11678174	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11682934	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11691670	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12469420	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12471390	0.85[EUR][1000 genomes]
rs3731935	0.91[MKK][hapmap]
rs4907237	0.87[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4907238	0.80[AMR][1000 genomes]
rs4907240	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907241	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4907242	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907246	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62154845	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62156200	0.81[AMR][1000 genomes]
rs66727130	0.85[EUR][1000 genomes]
rs6747149	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6749159	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6759099	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7575254	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7580048	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2278563	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs2278563	MGAT4A	cis	parietal	SCAN
rs2278563	CIAO1	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97203800-97220000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:97204200-97213200	Weak transcription	HSMMtube	muscle
3	chr2:97204400-97213000	Weak transcription	Ovary	ovary
4	chr2:97204400-97220000	Weak transcription	HSMM	muscle
5	chr2:97204600-97215200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:97204800-97215200	Weak transcription	Liver	Liver
7	chr2:97205200-97213000	Weak transcription	Gastric	stomach
8	chr2:97205200-97213200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:97205200-97213200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:97205200-97214200	Weak transcription	Pancreas	Pancrea
11	chr2:97205400-97213200	Weak transcription	Fetal Lung	lung
12	chr2:97205400-97215400	Weak transcription	HepG2	liver
13	chr2:97205600-97213000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:97205600-97213600	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr2:97205800-97213000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:97205800-97213200	Weak transcription	Fetal Intestine Small	intestine
17	chr2:97205800-97213400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:97205800-97215000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:97205800-97220000	Weak transcription	Primary B cells from cord blood	blood
20	chr2:97206000-97213000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:97206000-97213200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:97206000-97218800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:97206000-97220000	Weak transcription	Fetal Heart	heart
24	chr2:97206200-97213000	Weak transcription	Brain Substantia Nigra	brain
25	chr2:97206200-97213200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:97206200-97214400	Weak transcription	Brain Anterior Caudate	brain
27	chr2:97206200-97214600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:97206200-97215600	Weak transcription	A549	lung
29	chr2:97206400-97214400	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:97206600-97220000	Weak transcription	NHEK	skin
31	chr2:97206600-97222200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:97207200-97213800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:97207200-97219600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:97207400-97214400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:97207400-97214600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:97207600-97213000	Weak transcription	Osteobl	bone
37	chr2:97207600-97219600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:97207800-97213200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:97207800-97213200	Weak transcription	NHLF	lung
40	chr2:97207800-97219000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:97208000-97213000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:97208000-97219000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:97208600-97212800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:97208800-97213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:97208800-97213000	Weak transcription	Left Ventricle	heart
46	chr2:97208800-97213200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:97208800-97213600	Strong transcription	Aorta	Aorta
48	chr2:97209000-97213000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:97209000-97220400	Weak transcription	Psoas Muscle	Psoas
50	chr2:97209200-97213200	Weak transcription	NH-A	brain

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