Variant report

Variant	rs9344530
Chromosome Location	chr6:86192257-86192258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:86191926-86193820	SK-N-SH	brain:	n/a	chr6:86192977-86192998 chr6:86192984-86192997 chr6:86192982-86193000 chr6:86192983-86192999 chr6:86192984-86192997
2	EP300	chr6:86191983-86193286	SK-N-SH	brain:	n/a	n/a
3	EP300	chr6:86192083-86192637	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr6:86192030-86192674	SK-N-SH_RA	brain:	n/a	n/a
5	SIN3AK20	chr6:86192087-86192618	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr6:86192118-86192528	SK-N-SH	brain:	n/a	n/a
7	TAF1	chr6:86192244-86192522	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr6:86191902-86193397	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr6:86192032-86193356	SK-N-SH	brain:	n/a	chr6:86192980-86192999
10	MAX	chr6:86192059-86193212	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr6:86192194-86192801	U87	brain:	n/a	n/a
12	GATA3	chr6:86191974-86193304	SK-N-SH	brain:	n/a	chr6:86192898-86192906
13	SMC3	chr6:86191631-86193563	SK-N-SH	brain:	n/a	chr6:86192984-86192998
14	GATA3	chr6:86191920-86193304	SK-N-SH	brain:	n/a	chr6:86192898-86192906
15	MAX	chr6:86192038-86192712	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr6:86191999-86193200	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr6:86191947-86193318	SK-N-SH	brain:	n/a	chr6:86192413-86192430
18	RAD21	chr6:86192155-86193136	SK-N-SH_RA	brain:	n/a	chr6:86192980-86192999
19	STAT1	chr6:86192256-86193211	Hela-S3	cervix:	n/a	chr6:86192917-86192926 chr6:86192912-86192932 chr6:86192916-86192927 chr6:86192467-86192490 chr6:86192915-86192929 chr6:86192918-86192927
20	POLR2A	chr6:86192019-86193486	U87	brain:	n/a	n/a
21	POLR2A	chr6:86192051-86193455	U87	brain:	n/a	n/a
22	TEAD4	chr6:86192112-86193047	SK-N-SH	brain:	n/a	n/a
23	REST	chr6:86192218-86192663	SK-N-SH	brain:	n/a	n/a
24	TCF12	chr6:86191900-86193196	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr6:86191972-86193225	SK-N-SH	brain:	n/a	n/a
26	USF1	chr6:86192030-86192290	SK-N-SH_RA	brain:	n/a	n/a
27	POLR2A	chr6:86191808-86193320	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86191399..86193392-chr6:86300815..86302853,2	K562	blood:
2	chr6:86186911..86189535-chr6:86191240..86192894,2	K562	blood:

Variant related genes	Relation type
NT5E	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1000632	0.81[ASN][1000 genomes]
rs1000633	0.81[ASN][1000 genomes]
rs1000634	0.81[ASN][1000 genomes]
rs11508041	0.82[ASN][1000 genomes]
rs11963844	0.82[ASN][1000 genomes]
rs11968230	0.82[ASN][1000 genomes]
rs11968238	0.82[ASN][1000 genomes]
rs12055597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12524836	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs12528808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12664908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1322401	0.81[ASN][1000 genomes]
rs1570310	0.81[ASN][1000 genomes]
rs1570311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2208722	0.81[ASN][1000 genomes]
rs2229524	1.00[ASN][1000 genomes]
rs2295890	0.82[ASN][1000 genomes]
rs3812137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144166	0.87[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4327657	1.00[ASN][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs4400191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs4458647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4463232	0.82[ASN][1000 genomes]
rs4487548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs4571538	0.82[ASN][1000 genomes]
rs494688	0.85[JPT][hapmap]
rs59797285	0.82[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6902638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6902904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6910543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6913634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6923017	0.81[ASN][1000 genomes]
rs6930790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs73751215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7745560	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7746186	0.87[ASN][1000 genomes]
rs7749600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7749745	0.81[ASN][1000 genomes]
rs7752105	0.93[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7753936	0.81[ASN][1000 genomes]
rs7753950	0.81[ASN][1000 genomes]
rs7754559	0.81[ASN][1000 genomes]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7772233	0.82[ASN][1000 genomes]
rs7775788	0.81[ASN][1000 genomes]
rs9294336	0.82[ASN][1000 genomes]
rs9342039	0.82[ASN][1000 genomes]
rs9344519	0.81[ASN][1000 genomes]
rs9344520	0.81[ASN][1000 genomes]
rs9344521	0.81[ASN][1000 genomes]
rs9344522	0.81[ASN][1000 genomes]
rs9344523	0.82[ASN][1000 genomes]
rs9344524	0.82[ASN][1000 genomes]
rs9344525	0.82[ASN][1000 genomes]
rs9344526	0.82[ASN][1000 genomes]
rs9344527	0.87[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9344529	0.87[ASN][1000 genomes]
rs9344538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9351063	0.93[ASN][1000 genomes]
rs9353312	0.82[ASN][1000 genomes]
rs9353313	0.82[ASN][1000 genomes]
rs9353314	0.82[ASN][1000 genomes]
rs9353315	0.82[ASN][1000 genomes]
rs9353316	0.82[ASN][1000 genomes]
rs9353317	0.82[ASN][1000 genomes]
rs9353319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9353321	0.93[ASN][1000 genomes]
rs9353323	0.81[ASN][1000 genomes]
rs9353324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9359654	0.82[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs9359656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362211	0.81[ASN][1000 genomes]
rs9362213	0.81[ASN][1000 genomes]
rs9362215	0.81[ASN][1000 genomes]
rs9362216	0.82[ASN][1000 genomes]
rs9362217	0.82[ASN][1000 genomes]
rs9362218	0.82[ASN][1000 genomes]
rs9362219	0.82[ASN][1000 genomes]
rs9362220	0.82[ASN][1000 genomes]
rs9362221	0.82[ASN][1000 genomes]
rs9362223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9362224	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362225	1.00[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9444353	0.93[ASN][1000 genomes]
rs9450274	0.82[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9450279	0.82[ASN][1000 genomes]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9450286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450289	0.93[ASN][1000 genomes]
rs9450294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9450295	0.93[ASN][1000 genomes]
rs9450300	0.93[ASN][1000 genomes]
rs9450304	0.81[ASN][1000 genomes]
rs9450307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9450308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9450309	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised 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	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9344530	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs9344530	NT5E	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:86176200-86192400	Weak transcription	A549	lung
3	chr6:86176200-86192600	Weak transcription	HepG2	liver
4	chr6:86176800-86242600	Weak transcription	Gastric	stomach
5	chr6:86178800-86206800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:86183800-86192600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:86185200-86192400	Strong transcription	NHEK	skin
8	chr6:86185200-86192600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:86185400-86195600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:86186800-86194800	Weak transcription	Fetal Stomach	stomach
11	chr6:86186800-86196000	Weak transcription	Aorta	Aorta
12	chr6:86186800-86206200	Weak transcription	Lung	lung
13	chr6:86186800-86211000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:86189000-86195000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:86189200-86197800	Enhancers	Placenta	Placenta
16	chr6:86189800-86194200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:86189800-86194800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:86190000-86192600	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:86190000-86196200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:86190200-86192400	Weak transcription	HMEC	breast
21	chr6:86190200-86196200	Weak transcription	Liver	Liver
22	chr6:86190600-86193200	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr6:86191000-86193000	Enhancers	NHLF	lung
24	chr6:86191200-86192400	Weak transcription	HSMMtube	muscle
25	chr6:86191400-86193000	Enhancers	Fetal Intestine Small	intestine
26	chr6:86191400-86193200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:86191400-86200200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:86191600-86192400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:86191600-86194800	Genic enhancers	HSMM	muscle
30	chr6:86191800-86193000	Enhancers	Colon Smooth Muscle	Colon
31	chr6:86192000-86192400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:86192000-86192800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:86192000-86193000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:86192200-86192400	Enhancers	Stomach Smooth Muscle	stomach
35	chr6:86192200-86192600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:86192200-86192600	Enhancers	Right Atrium	heart
37	chr6:86192200-86192800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:86192200-86192800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:86192200-86192800	Enhancers	Ovary	ovary
40	chr6:86192200-86192800	Flanking Active TSS	NHDF-Ad	bronchial
41	chr6:86192200-86192800	Flanking Active TSS	Osteobl	bone
42	chr6:86192200-86193000	Enhancers	Small Intestine	intestine
43	chr6:86192200-86193000	Bivalent Enhancer	Stomach Mucosa	stomach
44	chr6:86192200-86193000	Enhancers	Hela-S3	cervix
45	chr6:86192200-86193000	Enhancers	NH-A	brain
46	chr6:86192200-86193200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:86192200-86193400	Enhancers	Rectal Smooth Muscle	rectum
48	chr6:86192200-86193400	Enhancers	HUVEC	blood vessel
49	chr6:86192200-86193600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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