Variant report

Variant	rs9986517
Chromosome Location	chr6:36719079-36719080
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36703852..36706817-chr6:36717625..36719969,2	K562	blood:
2	chr6:36577343..36580259-chr6:36718203..36721182,2	MCF-7	breast:
3	chr6:36572662..36574979-chr6:36718444..36721087,2	K562	blood:
4	chr6:36561092..36562918-chr6:36718882..36720382,2	MCF-7	breast:
5	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
6	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
7	chr6:36716404..36719581-chr6:36720288..36722523,3	MCF-7	breast:
8	chr6:36708140..36710606-chr6:36718569..36720077,2	MCF-7	breast:
9	chr6:36717988..36719917-chr6:36723476..36726910,3	MCF-7	breast:
10	chr6:36564984..36567276-chr6:36718585..36720409,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124772	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000220349	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs16889039	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1894560	0.84[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs190201	0.93[JPT][hapmap]
rs236451	0.87[ASN][1000 genomes]
rs236454	0.86[ASN][1000 genomes]
rs236455	0.86[ASN][1000 genomes]
rs236456	0.82[ASN][1000 genomes]
rs236458	0.86[ASN][1000 genomes]
rs236463	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs236464	0.82[ASN][1000 genomes]
rs236467	0.84[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs236468	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs236469	0.82[ASN][1000 genomes]
rs236470	0.92[JPT][hapmap]
rs236471	0.84[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs236472	0.84[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs3213534	0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213535	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70692	0.84[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs86702	0.81[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs86703	0.84[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs9462216	0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs9470386	0.85[CHB][hapmap]
rs9470387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv885809	chr6:36687518-36719079	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv885811	chr6:36695223-36719079	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv885814	chr6:36704807-36722842	Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv602951	chr6:36706157-36719079	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9986517	NUDT3	cis	cerebellum	SCAN
rs9986517	PIM1	cis	cerebellum	SCAN
rs9986517	SPDEF	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36704000-36720400	Weak transcription	Right Ventricle	heart
2	chr6:36708400-36720800	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr6:36709200-36727000	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:36711800-36719800	Weak transcription	Gastric	stomach
5	chr6:36716000-36719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:36717600-36721800	Enhancers	Stomach Mucosa	stomach
7	chr6:36718000-36719200	Enhancers	Esophagus	oesophagus
8	chr6:36718000-36719200	ZNF genes & repeats	Fetal Muscle Leg	muscle
9	chr6:36718000-36720600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:36718200-36721000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:36718200-36722200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:36718400-36719800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:36718400-36720600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:36718400-36720600	Enhancers	HMEC	breast
15	chr6:36718400-36721000	Weak transcription	Right Atrium	heart
16	chr6:36718400-36723400	Enhancers	Duodenum Mucosa	Duodenum
17	chr6:36718400-36723400	Enhancers	NHEK	skin
18	chr6:36718600-36719600	Weak transcription	Fetal Intestine Large	intestine
19	chr6:36718600-36719600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:36718600-36719800	Weak transcription	Spleen	Spleen
21	chr6:36718600-36722600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:36718600-36723200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:36718600-36724200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:36718600-36725400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:36718600-36725800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:36718600-36726600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:36718800-36719600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr6:36718800-36719800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:36718800-36719800	Weak transcription	Fetal Stomach	stomach
30	chr6:36718800-36723400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:36718800-36726800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:36718800-36727400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:36718800-36727400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:36719000-36719200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:36719000-36719200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:36719000-36719400	Weak transcription	Colonic Mucosa	Colon
37	chr6:36719000-36719800	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr6:36719000-36720000	Genic enhancers	Primary B cells from cord blood	blood

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