Variant report

Variant	rs1198846
Chromosome Location	chr2:10908233-10908234
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10908158..10909919-chr2:10911915..10914036,2	K562	blood:
2	chr2:10905694..10908583-chr2:10912957..10914642,3	MCF-7	breast:
3	chr2:10900619..10902721-chr2:10906421..10908391,2	MCF-7	breast:
4	chr2:10905922..10908917-chr2:10914932..10916687,3	MCF-7	breast:
5	chr2:10829824..10831420-chr2:10907947..10910452,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDIA6-1	chr2:10908001-10908322	ENSG00000272275.1

Variant related genes	Relation type
ENSG00000243819	Chromatin interaction
ENSG00000115761	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1198844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198845	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12464513	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477285	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046793	0.94[EUR][1000 genomes]
rs3856466	0.92[EUR][1000 genomes]
rs55648622	0.81[EUR][1000 genomes]
rs55675740	0.90[EUR][1000 genomes]
rs55906240	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56093996	0.80[EUR][1000 genomes]
rs56143168	0.92[EUR][1000 genomes]
rs56195743	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56264212	0.81[EUR][1000 genomes]
rs66538971	0.98[EUR][1000 genomes]
rs72777378	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72777379	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72777381	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72777384	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72777388	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72777393	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10903400-10914400	Weak transcription	Right Atrium	heart
2	chr2:10903600-10914400	Weak transcription	Gastric	stomach
3	chr2:10904200-10916400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:10904600-10916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:10904800-10915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:10905600-10918000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:10906000-10914200	Weak transcription	Esophagus	oesophagus
8	chr2:10906200-10908400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:10906200-10918200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:10906200-10918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:10906400-10912200	Weak transcription	Placenta	Placenta
12	chr2:10906400-10913000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:10908000-10908800	Enhancers	HSMM	muscle
14	chr2:10908000-10918200	Weak transcription	Pancreas	Pancrea
15	chr2:10908000-10918400	Weak transcription	Aorta	Aorta
16	chr2:10908200-10908400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:10908200-10908400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:10908200-10908400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:10908200-10908400	Enhancers	HSMMtube	muscle
20	chr2:10908200-10908600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:10908200-10908600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
22	chr2:10908200-10908600	Enhancers	Psoas Muscle	Psoas
23	chr2:10908200-10908800	Enhancers	Fetal Muscle Leg	muscle
24	chr2:10908200-10908800	Enhancers	Right Ventricle	heart
25	chr2:10908200-10908800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr2:10908200-10909000	Flanking Active TSS	Hela-S3	cervix
27	chr2:10908200-10909200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:10908200-10909400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:10908200-10909400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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