Variant report

Variant	rs9837256
Chromosome Location	chr3:61600528-61600529
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13323753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72890406	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72890413	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73111538	1.00[ASN][1000 genomes]
rs73111543	1.00[ASN][1000 genomes]
rs9852959	0.87[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription 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 miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv2756995	chr3:61569557-61636156	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	esv2759153	chr3:61569557-61636156	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv35004	chr3:61570149-61626426	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv822106	chr3:61577755-61631078	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv1001611	chr3:61598148-61686809	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1000158	chr3:61598562-61682888	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv1800730	chr3:61599495-61620573	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9837256	NCRNA00221	trans	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61581000-61609000	Weak transcription	NHEK	skin
2	chr3:61581400-61612200	Weak transcription	NHLF	lung
3	chr3:61581400-61613400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:61584400-61602200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:61584600-61602200	Weak transcription	Ovary	ovary
6	chr3:61586400-61614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:61586600-61602200	Weak transcription	Fetal Intestine Large	intestine
8	chr3:61587000-61611400	Weak transcription	HepG2	liver
9	chr3:61587800-61602600	Weak transcription	HSMMtube	muscle
10	chr3:61587800-61602800	Weak transcription	Gastric	stomach
11	chr3:61592000-61602600	Weak transcription	Fetal Intestine Small	intestine
12	chr3:61592800-61602400	Weak transcription	Fetal Stomach	stomach
13	chr3:61592800-61603000	Weak transcription	Fetal Lung	lung
14	chr3:61592800-61619800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:61593000-61601000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:61594400-61602000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:61594400-61610200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:61594600-61601000	Weak transcription	Right Ventricle	heart
19	chr3:61594600-61602800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:61594800-61605000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:61597400-61600600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:61598200-61601000	Weak transcription	Right Atrium	heart
23	chr3:61598200-61602200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:61598200-61602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:61598200-61602400	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:61598200-61602600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:61598200-61605000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:61598200-61605600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:61598200-61612200	Weak transcription	NHDF-Ad	bronchial
30	chr3:61598400-61600600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:61598400-61602200	Weak transcription	Liver	Liver
32	chr3:61598400-61602400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:61598400-61602600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:61598400-61602600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:61598400-61602800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:61598400-61611200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:61598600-61602600	Weak transcription	Fetal Heart	heart
38	chr3:61598600-61605400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:61598800-61600800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:61598800-61601400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:61598800-61602000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:61598800-61602200	Weak transcription	Lung	lung
43	chr3:61598800-61602600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:61598800-61603000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:61598800-61623200	Weak transcription	Aorta	Aorta
46	chr3:61599000-61602600	Weak transcription	Osteobl	bone
47	chr3:61599200-61602400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:61599400-61602800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:61599600-61602600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:61599600-61603000	Weak transcription	Fetal Brain Male	brain

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