Variant report

Variant	rs4832198
Chromosome Location	chr2:85995648-85995649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85995337..85997377-chr2:86000338..86004148,3	K562	blood:
2	chr2:85989917..85993093-chr2:85993435..85996690,4	MCF-7	breast:
3	chr2:85995032..85998218-chr2:85998499..86001360,4	MCF-7	breast:
4	chr2:85989736..85992227-chr2:85994375..85996424,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATOH8-3	chr2:85994919-85995836	l_1877_chr2:85969788-85975170_thyroid

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1055770	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs11688843	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989354	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001375	1.00[CHB][hapmap]
rs13009725	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13035450	1.00[CHB][hapmap]
rs1465821	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4832010	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832011	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4832012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832013	0.92[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832194	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832197	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832199	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs67494720	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1012593	chr2:85966323-85997189	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv535806	chr2:85990408-86007918	Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4832198	GNLY	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85986000-85995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:85987000-85998400	Genic enhancers	Muscle Satellite Cultured Cells	--
3	chr2:85988000-85996200	Enhancers	Hela-S3	cervix
4	chr2:85988600-86000000	Enhancers	Right Atrium	heart
5	chr2:85990800-85995800	Enhancers	Fetal Heart	heart
6	chr2:85990800-85999800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr2:85991000-85997600	Genic enhancers	Lung	lung
8	chr2:85991000-85997800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:85991200-86000000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr2:85992800-85997200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:85993000-85997000	Genic enhancers	HSMM	muscle
12	chr2:85993400-85998200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:85993400-86000000	Enhancers	Psoas Muscle	Psoas
14	chr2:85993600-85995800	Weak transcription	Fetal Brain Male	brain
15	chr2:85993800-85997200	Genic enhancers	Right Ventricle	heart
16	chr2:85993800-85998000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:85994000-85996200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:85994000-85996400	Weak transcription	HepG2	liver
19	chr2:85994000-85998600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:85994000-86000400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:85994200-86000000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:85994400-85998600	Genic enhancers	Fetal Lung	lung
23	chr2:85994400-85999000	Enhancers	Left Ventricle	heart
24	chr2:85994600-85996000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:85994800-85997000	Genic enhancers	Aorta	Aorta
26	chr2:85994800-85997400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:85994800-85998800	Enhancers	HSMMtube	muscle
28	chr2:85994800-86002200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:85995000-85995800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:85995000-85995800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
31	chr2:85995000-85996000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:85995000-85996000	Enhancers	Esophagus	oesophagus
33	chr2:85995000-85996400	Enhancers	Colon Smooth Muscle	Colon
34	chr2:85995000-85996800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:85995000-85996800	Enhancers	Gastric	stomach
36	chr2:85995000-85997000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:85995000-85997400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:85995000-85997800	Genic enhancers	Fetal Stomach	stomach
39	chr2:85995000-85998800	Enhancers	Brain Hippocampus Middle	brain
40	chr2:85995000-85999000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:85995000-85999000	Enhancers	Colonic Mucosa	Colon
42	chr2:85995200-85995800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:85995200-85996200	Genic enhancers	Brain Anterior Caudate	brain
44	chr2:85995200-85996200	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:85995200-85997600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr2:85995200-85998200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr2:85995200-85998400	Enhancers	Spleen	Spleen
48	chr2:85995200-85999000	Enhancers	Fetal Muscle Leg	muscle
49	chr2:85995200-85999200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:85995200-85999800	Enhancers	NHDF-Ad	bronchial

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