Variant report

Variant	rs6542925
Chromosome Location	chr2:100898081-100898082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100896929..100899724-chr2:100932462..100934829,2	K562	blood:
2	chr2:100895235..100899399-chr2:100936905..100939740,4	K562	blood:
3	chr2:100889062..100891590-chr2:100897869..100900179,3	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10174820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176062	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10176143	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10195018	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10201565	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10201669	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11890655	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902303	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12612755	0.81[ASN][1000 genomes]
rs12615454	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13391517	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13400045	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13409545	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17023901	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17023916	0.80[CEU][hapmap]
rs3748928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4322861	0.82[ASN][1000 genomes]
rs4850925	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851278	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4851279	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs55759234	0.81[AMR][1000 genomes]
rs6542922	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs7556910	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7571306	0.81[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6542925	IL18RAP	cis	parietal	SCAN
rs6542925	NMS	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:100880200-100898400	Weak transcription	A549	lung
3	chr2:100884200-100900200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:100885600-100898200	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:100887000-100900200	Weak transcription	Left Ventricle	heart
7	chr2:100887800-100901800	Weak transcription	Fetal Intestine Small	intestine
8	chr2:100889400-100900200	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:100889600-100898200	Weak transcription	Fetal Brain Male	brain
10	chr2:100889600-100898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:100890600-100900200	Weak transcription	Right Ventricle	heart
12	chr2:100891400-100900000	Weak transcription	Aorta	Aorta
13	chr2:100891800-100900200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:100892000-100898600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:100892000-100902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:100892000-100904000	Weak transcription	Gastric	stomach
18	chr2:100892200-100898200	Weak transcription	Brain Germinal Matrix	brain
19	chr2:100892200-100900200	Weak transcription	Pancreas	Pancrea
20	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:100892400-100900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:100894400-100900400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:100895600-100900200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:100896600-100899000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:100896600-100900000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:100896600-100907000	Weak transcription	Spleen	Spleen
27	chr2:100896600-100907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:100896800-100898200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:100896800-100898400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:100896800-100898800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:100897000-100898200	Weak transcription	Ovary	ovary
32	chr2:100897400-100898800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr2:100897400-100899000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr2:100897400-100899000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:100897600-100899000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:100897600-100899000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:100897600-100903600	Enhancers	Dnd41	blood
38	chr2:100897800-100898400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:100897800-100898400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr2:100897800-100898600	Flanking Active TSS	K562	blood
41	chr2:100897800-100898800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:100897800-100898800	Enhancers	NH-A	brain
43	chr2:100898000-100898200	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr2:100898000-100898200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr2:100898000-100898200	Active TSS	Adipose Nuclei	Adipose
46	chr2:100898000-100898400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:100898000-100898400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr2:100898000-100898400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:100898000-100898400	Enhancers	Fetal Lung	lung
50	chr2:100898000-100898400	Enhancers	Fetal Stomach	stomach

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