Variant report

Variant	rs6754867
Chromosome Location	chr2:100895081-100895082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100893699..100897169-chr2:100899587..100903259,4	MCF-7	breast:
2	chr2:100881197..100884068-chr2:100895021..100897043,2	K562	blood:
3	chr2:100893591..100896476-chr2:100936807..100939539,2	K562	blood:
4	chr2:100889734..100892387-chr2:100894047..100896646,2	K562	blood:
5	chr2:100893081..100895089-chr2:100906389..100909363,2	MCF-7	breast:
6	chr2:100893922..100895614-chr2:100937992..100940398,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST10-2	chr2:100892673-100898479	NONHSAT072773

No data

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10865039	0.81[ASN][1000 genomes]
rs12464505	1.00[JPT][hapmap]
rs12467008	1.00[JPT][hapmap]
rs13024601	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2309815	1.00[JPT][hapmap]
rs2309817	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2309818	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs2309819	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2309820	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2309821	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2309822	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2309823	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2309824	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2309825	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2309826	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2871341	1.00[JPT][hapmap]
rs4561689	0.81[ASN][1000 genomes]
rs4851281	1.00[JPT][hapmap]
rs4851282	1.00[JPT][hapmap]
rs4851283	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851284	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4851285	0.81[ASN][1000 genomes]
rs6542923	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542924	1.00[CHB][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6755791	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7421891	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7559464	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7562372	1.00[CHB][hapmap]
rs7588623	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7601873	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7607170	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7609376	0.81[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6754867	LONRF2	cis	parietal	SCAN
rs6754867	LONRF2	cis	cerebellum	SCAN
rs6754867	CNGA3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100879400-100896200	Weak transcription	Spleen	Spleen
2	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:100880200-100898400	Weak transcription	A549	lung
4	chr2:100884200-100900200	Weak transcription	Brain Angular Gyrus	brain
5	chr2:100884800-100897400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:100885600-100898200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:100887000-100900200	Weak transcription	Left Ventricle	heart
9	chr2:100887200-100898000	Weak transcription	Fetal Brain Female	brain
10	chr2:100887800-100901800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:100888000-100898000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:100888200-100896000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:100889400-100900200	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:100889600-100898200	Weak transcription	Fetal Brain Male	brain
15	chr2:100889600-100898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:100890600-100900200	Weak transcription	Right Ventricle	heart
17	chr2:100891400-100900000	Weak transcription	Aorta	Aorta
18	chr2:100891600-100896000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:100891800-100900200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:100892000-100896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:100892000-100896200	Weak transcription	Ovary	ovary
23	chr2:100892000-100898000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:100892000-100898600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:100892000-100902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:100892000-100904000	Weak transcription	Gastric	stomach
27	chr2:100892200-100895400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:100892200-100898200	Weak transcription	Brain Germinal Matrix	brain
29	chr2:100892200-100900200	Weak transcription	Pancreas	Pancrea
30	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:100892400-100900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:100894400-100900400	Weak transcription	Brain Anterior Caudate	brain
33	chr2:100894600-100897600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:100894800-100896200	Enhancers	Dnd41	blood
35	chr2:100894800-100896600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:100895000-100895400	Enhancers	K562	blood

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