Variant report

Variant	rs1198872
Chromosome Location	chr2:10903412-10903413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10875606..10877816-chr2:10902638..10905223,2	MCF-7	breast:
2	chr2:10902093..10904756-chr2:10950364..10952996,3	MCF-7	breast:
3	chr2:10859131..10862266-chr2:10901293..10904159,3	MCF-7	breast:
4	chr2:10897911..10900939-chr2:10902372..10905567,4	MCF-7	breast:
5	chr2:10902594..10905238-chr2:10911928..10914865,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143870	Chromatin interaction
ENSG00000143882	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10427170	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1198859	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198860	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198861	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198862	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198863	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198864	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198866	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198867	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1198868	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1198869	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198870	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers 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	21 gene(s)	inside rSNPs	diseases
4	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv3427047	chr2:10900130-10906802	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cardiac Troponin-T levels	23247143	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1198872	C2orf50	cis	parietal	SCAN
rs1198872	ASAP2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10892600-10905400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:10897800-10906400	Enhancers	Placenta	Placenta
3	chr2:10899800-10905200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:10899800-10908200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:10900000-10905000	Weak transcription	Fetal Intestine Large	intestine
6	chr2:10900000-10905400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:10902200-10905400	Weak transcription	Esophagus	oesophagus
8	chr2:10902800-10903600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:10902800-10903600	Enhancers	Pancreas	Pancrea
10	chr2:10902800-10903600	Enhancers	Right Ventricle	heart
11	chr2:10902800-10903800	Enhancers	Fetal Heart	heart
12	chr2:10902800-10903800	Enhancers	Lung	lung
13	chr2:10902800-10903800	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr2:10902800-10904000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr2:10902800-10904400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:10903000-10903600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:10903000-10903800	Enhancers	Fetal Intestine Small	intestine
18	chr2:10903000-10903800	Enhancers	Left Ventricle	heart
19	chr2:10903000-10904600	Enhancers	Spleen	Spleen
20	chr2:10903200-10903600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:10903200-10905000	Weak transcription	Hela-S3	cervix
22	chr2:10903400-10903600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:10903400-10903600	Enhancers	Gastric	stomach
24	chr2:10903400-10904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:10903400-10904400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:10903400-10908200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:10903400-10908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:10903400-10914400	Weak transcription	Right Atrium	heart

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