Variant report

Variant	rs3755248
Chromosome Location	chr2:188370232-188370233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:188367651..188372772-chr2:188414874..188419301,6	K562	blood:
2	chr2:188368955..188371760-chr2:188416561..188418698,2	K562	blood:
3	chr2:188367231..188371096-chr2:188401019..188405423,6	K562	blood:
4	chr2:188362083..188363643-chr2:188369549..188371149,2	K562	blood:

Variant related genes	Relation type
ENSG00000003436	Chromatin interaction
ENSG00000224063	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10172935	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179705	0.84[CHD][hapmap]
rs11674362	0.83[CHD][hapmap]
rs13408875	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355519	0.84[CHD][hapmap]
rs2041778	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs2192823	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2300412	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2349653	0.97[ASN][1000 genomes]
rs34607903	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7572886	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586970	0.84[CHD][hapmap]
rs7591567	0.84[CHD][hapmap]
rs7598858	0.84[CHD][hapmap]
rs8176479	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs8176541	0.84[CHD][hapmap]
rs8176546	0.84[CHD][hapmap]
rs8176548	0.88[CHD][hapmap]
rs8176580	0.84[CHD][hapmap]
rs8176583	0.84[CHD][hapmap]
rs8176592	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875557	chr2:188219052-188370232	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv875558	chr2:188219052-188388311	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv875559	chr2:188219052-188390112	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv875562	chr2:188258904-188370232	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv875563	chr2:188258904-188388311	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875564	chr2:188258904-188414161	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875565	chr2:188258904-188440752	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv875566	chr2:188258904-188626214	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv875567	chr2:188258904-188673462	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription 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 miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv834488	chr2:188268434-188415496	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv875568	chr2:188291105-188653806	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv875576	chr2:188343497-188482933	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv875577	chr2:188343497-188500930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv875578	chr2:188343497-188690187	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv997899	chr2:188356689-188531831	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1014298	chr2:188359747-188531831	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1013166	chr2:188359747-188544803	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1014942	chr2:188360116-188480738	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv584038	chr2:188370232-188450136	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv875580	chr2:188370232-188521234	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	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
rs3755248	C2orf88	cis	parietal	SCAN
rs3755248	ORMDL1	cis	cerebellum	SCAN
rs3755248	CALCRL	cis	cerebellum	SCAN
rs3755248	CALCRL	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188334200-188374600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:188356400-188374400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:188358400-188374600	Weak transcription	Fetal Thymus	thymus
4	chr2:188359200-188375600	Weak transcription	Lung	lung
5	chr2:188360600-188375600	Weak transcription	HSMMtube	muscle
6	chr2:188360600-188391600	Weak transcription	Psoas Muscle	Psoas
7	chr2:188365400-188370400	Enhancers	Hela-S3	cervix
8	chr2:188365400-188370600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:188365600-188376400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:188366200-188375400	Weak transcription	Placenta	Placenta
11	chr2:188367200-188374600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:188367200-188383800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:188367600-188381600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:188368200-188370600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:188368200-188374400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:188368400-188383800	Weak transcription	Osteobl	bone
17	chr2:188368600-188370400	Enhancers	Primary T cells from cord blood	blood
18	chr2:188368600-188370600	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:188368800-188374600	Weak transcription	HSMM	muscle
20	chr2:188369000-188370400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:188369000-188370600	Enhancers	Dnd41	blood
22	chr2:188369200-188374800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:188369400-188370400	Enhancers	K562	blood
24	chr2:188369600-188370400	Enhancers	HUVEC	blood vessel
25	chr2:188369600-188374600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:188369800-188370400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:188369800-188370600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:188370000-188370400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:188370000-188370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:188370000-188370800	Enhancers	A549	lung
31	chr2:188370000-188389800	Weak transcription	NHDF-Ad	bronchial
32	chr2:188370200-188370400	Flanking Active TSS	HepG2	liver
33	chr2:188370200-188370600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr2:188370200-188373800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:188370200-188374600	Weak transcription	Small Intestine	intestine
36	chr2:188370200-188375400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:188370200-188375600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:188370200-188375600	Weak transcription	Left Ventricle	heart
39	chr2:188370200-188378800	Weak transcription	Fetal Lung	lung

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