Variant report

Variant	rs2065114
Chromosome Location	chr6:86159143-86159144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:118)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:118 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr6:86158845-86160496	SK-N-SH	brain:	n/a	n/a
2	EP300	chr6:86159035-86159566	GM12878	blood:	n/a	chr6:86159349-86159363
3	PAX5	chr6:86158988-86159427	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:86159138-86160328	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:86159039-86160101	GM12892	blood:	n/a	n/a
6	SPI1	chr6:86159004-86159367	GM12891	blood:	n/a	n/a
7	SP1	chr6:86158931-86159680	GM12878	blood:	n/a	chr6:86159338-86159352 chr6:86159337-86159349 chr6:86159339-86159348
8	E2F6	chr6:86159056-86160381	H1-hESC	embryonic stem cell:	n/a	chr6:86159151-86159160 chr6:86159336-86159348
9	CHD1	chr6:86158995-86160647	GM12878	blood:	n/a	chr6:86159789-86159799 chr6:86159462-86159472 chr6:86159818-86159828
10	POLR2A	chr6:86159012-86160615	HUVEC	blood vessel:	n/a	n/a
11	ATF2	chr6:86158918-86160044	GM12878	blood:	n/a	chr6:86159672-86159683
12	EBF1	chr6:86159117-86159404	GM12878	blood:	n/a	n/a
13	RUNX3	chr6:86158936-86160509	GM12878	blood:	n/a	chr6:86159390-86159399 chr6:86159390-86159405
14	CUX1	chr6:86158988-86159704	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:86159028-86160547	GM12892	blood:	n/a	n/a
16	POLR2A	chr6:86159101-86160075	SK-N-SH	brain:	n/a	n/a
17	ATF2	chr6:86159112-86159556	GM12878	blood:	n/a	n/a
18	NRF1	chr6:86159083-86159670	GM12878	blood:	n/a	n/a
19	REST	chr6:86158954-86159499	SK-N-SH	brain:	n/a	chr6:86159087-86159096 chr6:86159087-86159100
20	POLR2A	chr6:86159028-86160479	GM19193	blood:	n/a	n/a
21	PAX5	chr6:86158955-86159406	GM12891	blood:	n/a	n/a
22	TAF1	chr6:86159060-86159554	GM12878	blood:	n/a	n/a
23	TAF1	chr6:86159004-86160525	SK-N-SH	brain:	n/a	n/a
24	RFX5	chr6:86159126-86160020	GM12878	blood:	n/a	n/a
25	MXI1	chr6:86158993-86161139	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:86159063-86159461	GM12892	blood:	n/a	n/a
27	POLR2A	chr6:86159029-86160358	H1-neurons	neurons:	n/a	n/a
28	TAF1	chr6:86159124-86160272	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr6:86158912-86160723	IMR90	lung:	n/a	chr6:86160263-86160275
30	MTA3	chr6:86159070-86159523	GM12878	blood:	n/a	n/a
31	ETS1	chr6:86158958-86159442	GM12878	blood:	n/a	chr6:86159222-86159235
32	EP300	chr6:86158952-86160225	SK-N-SH	brain:	n/a	chr6:86159349-86159363
33	POLR2A	chr6:86159045-86160513	GM18951	blood:	n/a	n/a
34	PAX5	chr6:86158985-86159672	GM12892	blood:	n/a	n/a
35	ZNF143	chr6:86159074-86160610	GM12878	blood:	n/a	chr6:86160209-86160219
36	MAX	chr6:86158964-86160254	SK-N-SH	brain:	n/a	chr6:86159340-86159350
37	POLR2A	chr6:86158913-86160237	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr6:86159123-86160302	Hela-S3	cervix:	n/a	n/a
39	ZNF384	chr6:86159097-86159433	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:86158885-86164174	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr6:86159110-86159359	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:86159002-86160149	GM12892	blood:	n/a	n/a
43	POLR2A	chr6:86158885-86160238	GM12878	blood:	n/a	n/a
44	RELA	chr6:86159046-86160479	GM18951	blood:	n/a	n/a
45	BCLAF1	chr6:86158990-86159383	GM12878	blood:	n/a	chr6:86159086-86159094
46	POLR2A	chr6:86159114-86160202	Gliobla	brain:	n/a	n/a
47	PAX5	chr6:86158986-86160094	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:86158918-86160716	ProgFib	skin:	n/a	n/a
49	BATF	chr6:86159141-86159373	GM12878	blood:	n/a	n/a
50	MAFK	chr6:86159107-86159964	IMR90	lung:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:86159096-86159146	BE2_C	brain:	n/a
2	chr6:86159103-86159153	BJ	skin:	n/a
3	chr6:86159103-86159153	NH-A	brain:	n/a
4	chr6:86159096-86159146	IMR90	lung:	fetal
5	chr6:86159096-86159146	MCF-7	breast:	n/a
6	chr6:86159103-86159153	MCF10A-Er-Src	breast:	n/a
7	chr6:86159096-86159146	GM06990	blood:	n/a
8	chr6:86159096-86159146	ovcar-3	ovarian:	n/a
9	chr6:86159103-86159153	AoSMC	blood vessel:	n/a
10	chr6:86159096-86159146	Caco-2	colon:	n/a
11	chr6:86159096-86159146	HAEpiC	amniotic membrane:	n/a
12	chr6:86159103-86159153	AG04449	skin:	fetal
13	chr6:86159103-86159153	HPAEpiC	pulmonary alveolar:	n/a
14	chr6:86159096-86159146	HCT-116	colon:	n/a
15	chr6:86159096-86159146	SKMC	muscle:	n/a
16	chr6:86159103-86159153	A549	lung:	n/a
17	chr6:86159103-86159153	HUVEC	blood vessel:	n/a
18	chr6:86159096-86159146	ProgFib	skin:	n/a
19	chr6:86159103-86159153	HEEpiC	esophagus:	n/a
20	chr6:86159103-86159153	SK-N-SH	brain:	n/a
21	chr6:86159103-86159153	HCF	heart:	n/a
22	chr6:86159103-86159153	NT2-D1	testis:	n/a
23	chr6:86159096-86159146	HCF	heart:	n/a
24	chr6:86159096-86159146	Jurkat	blood:	n/a
25	chr6:86159096-86159146	BJ	skin:	n/a
26	chr6:86159103-86159153	HepG2	liver:	n/a
27	chr6:86159096-86159146	HepG2	liver:	n/a
28	chr6:86159103-86159153	CMK	blood:	n/a
29	chr6:86159103-86159153	HCPEpiC	choroid plexus:	n/a
30	chr6:86159103-86159153	AG09309	skin:	n/a
31	chr6:86159103-86159153	Hela-S3	cervix:	n/a
32	chr6:86159103-86159153	LNCaP	prostate:	n/a
33	chr6:86159096-86159146	MCF10A-Er-Src	breast:	n/a
34	chr6:86159103-86159153	U87	brain:	n/a
35	chr6:86159096-86159146	GM19239	blood:	n/a
36	chr6:86159103-86159153	GM12891	blood:	n/a
37	chr6:86159096-86159146	HMEC	breast:	n/a
38	chr6:86159103-86159153	SKMC	muscle:	n/a
39	chr6:86159103-86159153	Caco-2	colon:	n/a
40	chr6:86159103-86159153	HRE	kidney:	n/a
41	chr6:86159096-86159146	HPAEpiC	pulmonary alveolar:	n/a
42	chr6:86159096-86159146	U87	brain:	n/a
43	chr6:86159096-86159146	ECC-1	luminal epithelium:	n/a
44	chr6:86159103-86159153	BE2_C	brain:	n/a
45	chr6:86159103-86159153	HRPEpiC	eye:	n/a
46	chr6:86159096-86159146	HRCEpiC	kidney:	n/a
47	chr6:86159096-86159146	H1-hESC	embryonic stem cell:	embryo
48	chr6:86159103-86159153	H1-hESC	embryonic stem cell:	embryo
49	chr6:86159096-86159146	A549	lung:	n/a
50	chr6:86159096-86159146	AG04450	lung:	fetal

No data

Variant related genes	Relation type
NT5E	TF binding region
NT5E	CpG island

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12199873	0.91[CHB][hapmap]
rs1590281	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181187	0.81[EUR][1000 genomes]
rs2208725	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229523	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2758840	0.91[CHB][hapmap]
rs2758846	0.91[CHB][hapmap]
rs2758847	0.91[CHB][hapmap]
rs2842601	0.86[CHB][hapmap]
rs2842604	0.91[CHB][hapmap]
rs2842607	0.91[CHB][hapmap]
rs2842608	0.91[CHB][hapmap]
rs2842612	0.91[CHB][hapmap]
rs2842613	0.91[CHB][hapmap]
rs3812133	0.86[CHB][hapmap]
rs4235826	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4235827	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4282381	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304137	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs4351223	0.91[CHB][hapmap]
rs4373337	0.86[CEU][hapmap]
rs4419647	0.82[ASN][1000 genomes]
rs4441928	0.91[CHB][hapmap]
rs4501401	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4562107	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4579322	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4593336	0.86[CEU][hapmap]
rs4707207	0.86[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454467	0.82[EUR][1000 genomes]
rs6454468	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454469	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6454471	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs6922	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs6931295	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7452605	0.91[CHB][hapmap]
rs7739563	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7746065	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765636	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7770359	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9294337	0.91[CHB][hapmap]
rs9344532	0.91[CHB][hapmap]
rs9353318	0.91[CHB][hapmap]
rs9362230	0.91[CHB][hapmap]
rs9444349	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450272	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2065114	SNHG5	cis	lung	GTEx
rs2065114	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2065114	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs2065114	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2065114	SNHG5	cis	Whole Blood	GTEx
rs2065114	SNHG5	cis	Muscle Skeletal	GTEx
rs2065114	SNHG5	cis	Thyroid	GTEx
rs2065114	SNHG5	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86145400-86159200	Weak transcription	Gastric	stomach
2	chr6:86157600-86159200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr6:86157800-86162200	Active TSS	Stomach Smooth Muscle	stomach
4	chr6:86157800-86162400	Active TSS	Colon Smooth Muscle	Colon
5	chr6:86158000-86161200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:86158000-86162000	Active TSS	Aorta	Aorta
7	chr6:86158200-86160000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:86158200-86162600	Active TSS	NHLF	lung
9	chr6:86158400-86159200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:86158400-86159200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
11	chr6:86158400-86162600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:86158600-86159200	Bivalent Enhancer	Fetal Thymus	thymus
13	chr6:86158600-86159200	Flanking Active TSS	HUVEC	blood vessel
14	chr6:86158600-86159400	Flanking Active TSS	HepG2	liver
15	chr6:86158600-86160200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr6:86158600-86160200	Active TSS	Brain Hippocampus Middle	brain
17	chr6:86158600-86160800	Active TSS	Brain Substantia Nigra	brain
18	chr6:86158600-86161400	Active TSS	Psoas Muscle	Psoas
19	chr6:86158600-86161400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:86158600-86161600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:86158600-86161600	Active TSS	Ovary	ovary
22	chr6:86158800-86159200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:86158800-86159400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:86158800-86159400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:86158800-86159800	Active TSS	Right Atrium	heart
26	chr6:86158800-86160000	Active TSS	Muscle Satellite Cultured Cells	--
27	chr6:86158800-86160400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:86158800-86160400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:86158800-86160600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:86158800-86160600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:86158800-86160800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr6:86158800-86160800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr6:86158800-86161000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr6:86158800-86161400	Active TSS	NH-A	brain
35	chr6:86158800-86161400	Active TSS	Osteobl	bone
36	chr6:86158800-86161600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr6:86158800-86161600	Active TSS	A549	lung
38	chr6:86158800-86161600	Active TSS	HMEC	breast
39	chr6:86158800-86161600	Active TSS	HSMM	muscle
40	chr6:86158800-86161600	Active TSS	HSMMtube	muscle
41	chr6:86158800-86162000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:86158800-86162000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:86158800-86162000	Active TSS	Rectal Smooth Muscle	rectum
44	chr6:86158800-86162000	Active TSS	GM12878-XiMat	blood
45	chr6:86158800-86162600	Active TSS	NHDF-Ad	bronchial
46	chr6:86159000-86159200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:86159000-86159200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr6:86159000-86159200	Active TSS	Primary T cells from cord blood	blood
49	chr6:86159000-86159200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:86159000-86159200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood

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