Variant report

Variant	rs9868705
Chromosome Location	chr3:196337197-196337198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196336063..196338579-chr3:196359293..196361189,3	MCF-7	breast:
2	chr3:196336240..196338630-chr3:196392949..196395877,2	K562	blood:
3	chr3:196336135..196338405-chr3:196439532..196442139,2	K562	blood:
4	chr3:196334907..196337248-chr3:196375808..196377333,2	K562	blood:
5	chr3:196330580..196333990-chr3:196334226..196339571,6	K562	blood:
6	chr3:196336450..196339251-chr3:196363480..196365260,2	K562	blood:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction
ENSG00000163964	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11719820	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12718060	0.86[ASN][1000 genomes]
rs13075023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075160	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1973264	0.86[ASN][1000 genomes]
rs4916511	0.81[EUR][1000 genomes]
rs4916512	0.82[EUR][1000 genomes]
rs6763582	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798553	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs6809251	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7629845	0.91[JPT][hapmap]
rs9883029	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][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	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
10	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9868705	MUC20	cis	lymphoblastoid	seeQTL
rs9868705	NCBP2	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196331800-196337400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:196331800-196339000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:196331800-196339200	Weak transcription	Right Atrium	heart
4	chr3:196336000-196338800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:196336000-196339200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:196336000-196340200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:196336200-196337200	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:196336200-196337200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:196336200-196337400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:196336200-196339800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr3:196336200-196339800	Enhancers	Placenta	Placenta
12	chr3:196336200-196341000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:196336400-196337200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:196336400-196337200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr3:196336400-196337200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:196336400-196337200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:196336400-196337200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:196336400-196337200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:196336400-196337200	Enhancers	Colon Smooth Muscle	Colon
20	chr3:196336400-196337200	Enhancers	Fetal Intestine Large	intestine
21	chr3:196336400-196337200	Enhancers	Fetal Muscle Leg	muscle
22	chr3:196336400-196337200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:196336400-196337200	Flanking Active TSS	Dnd41	blood
24	chr3:196336400-196337200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr3:196336400-196337400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:196336400-196337400	Enhancers	K562	blood
27	chr3:196336400-196337600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:196336400-196337600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:196336400-196339200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:196336400-196339800	Enhancers	Adipose Nuclei	Adipose
31	chr3:196336600-196337200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:196336600-196337200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:196336600-196337200	Enhancers	Stomach Mucosa	stomach
34	chr3:196336600-196338800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:196336600-196338800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:196336600-196339000	Weak transcription	Brain Substantia Nigra	brain
37	chr3:196336600-196339200	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:196336800-196337200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr3:196336800-196337200	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr3:196336800-196337200	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:196336800-196337200	Enhancers	Gastric	stomach
42	chr3:196336800-196337200	Enhancers	Left Ventricle	heart
43	chr3:196336800-196337200	Enhancers	Right Ventricle	heart
44	chr3:196336800-196337200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:196336800-196337200	Enhancers	Spleen	Spleen
46	chr3:196336800-196337200	Enhancers	GM12878-XiMat	blood
47	chr3:196336800-196337200	Flanking Active TSS	Hela-S3	cervix
48	chr3:196336800-196337400	Enhancers	Lung	lung
49	chr3:196336800-196337400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:196336800-196337400	Enhancers	Thymus	Thymus

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