Variant report

Variant	rs7678308
Chromosome Location	chr4:119199890-119199891
allele	C/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	TBL1XR1	chr4:119199569-119200796	K562	blood:	n/a	n/a
2	PML	chr4:119199445-119200406	K562	blood:	n/a	n/a
3	NR2F2	chr4:119199436-119200288	K562	blood:	n/a	n/a
4	BACH1	chr4:119199686-119200202	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr4:119197988-119206014	GM12878	blood:	n/a	n/a
6	MAX	chr4:119199549-119200437	Hela-S3	cervix:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
7	TAF1	chr4:119199465-119200328	Hela-S3	cervix:	n/a	n/a
8	TAF1	chr4:119199558-119201099	PFSK-1	brain:	n/a	n/a
9	GABPA	chr4:119199634-119199979	HepG2	liver:	n/a	chr4:119199690-119199699 chr4:119199690-119199701 chr4:119199687-119199701
10	MYBL2	chr4:119199192-119200727	HepG2	liver:	n/a	n/a
11	HEY1	chr4:119199447-119200795	K562	blood:	n/a	chr4:119199793-119199808
12	JUN	chr4:119199488-119200389	K562	blood:	n/a	chr4:119199812-119199821
13	TAF7	chr4:119199837-119200085	K562	blood:	n/a	n/a
14	TAF1	chr4:119199619-119200116	H1-neurons	neurons:	n/a	n/a
15	EP300	chr4:119199556-119199979	H1-hESC	embryonic stem cell:	n/a	chr4:119199594-119199603 chr4:119199817-119199830
16	GTF2F1	chr4:119199571-119200086	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr4:119199465-119200504	ECC-1	luminal epithelium:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
18	ZBTB33	chr4:119199755-119200029	A549	lung:	n/a	n/a
19	USF2	chr4:119199542-119200536	H1-hESC	embryonic stem cell:	n/a	chr4:119199711-119199722
20	FOXM1	chr4:119199372-119200960	GM12878	blood:	n/a	n/a
21	JUND	chr4:119199542-119200845	K562	blood:	n/a	chr4:119199812-119199821
22	TAF1	chr4:119199660-119200167	PFSK-1	brain:	n/a	n/a
23	E2F6	chr4:119199478-119200038	H1-hESC	embryonic stem cell:	n/a	chr4:119199691-119199700
24	MTA3	chr4:119199317-119200797	GM12878	blood:	n/a	n/a
25	EGR1	chr4:119199457-119200493	HCT-116	colon:	n/a	chr4:119199742-119199752 chr4:119199767-119199781 chr4:119199740-119199753 chr4:119199740-119199753 chr4:119199741-119199755 chr4:119199740-119199754 chr4:119199739-119199754 chr4:119199691-119199700
26	POLR2A	chr4:119198979-119204800	PBDE	blood:	n/a	n/a
27	POLR2A	chr4:119199784-119200287	A549	lung:	n/a	n/a
28	CBX3	chr4:119199510-119200398	K562	blood:	n/a	n/a
29	YY1	chr4:119199237-119200425	GM12878	blood:	n/a	chr4:119199745-119199756 chr4:119200221-119200233
30	SIN3AK20	chr4:119199784-119200286	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr4:119199360-119200410	MCF-7	breast:	n/a	n/a
32	MYC	chr4:119199635-119200302	HUVEC	blood vessel:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
33	TBL1XR1	chr4:119199604-119202467	K562	blood:	n/a	n/a
34	ZMIZ1	chr4:119199549-119200376	K562	blood:	n/a	n/a
35	MYC	chr4:119199465-119200393	Hela-S3	cervix:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
36	ELF1	chr4:119199523-119200065	HepG2	liver:	n/a	n/a
37	PML	chr4:119199506-119200473	GM12878	blood:	n/a	n/a
38	POLR2A	chr4:119199362-119200787	HepG2	liver:	n/a	n/a
39	MAX	chr4:119199497-119200553	HepG2	liver:	n/a	chr4:119199734-119199749 chr4:119199711-119199722
40	TAF1	chr4:119199239-119200450	K562	blood:	n/a	n/a
41	TBP	chr4:119199486-119200360	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF7	chr4:119199795-119200309	K562	blood:	n/a	n/a
43	CEBPB	chr4:119199687-119200136	K562	blood:	n/a	n/a
44	USF1	chr4:119199521-119199980	H1-hESC	embryonic stem cell:	n/a	n/a
45	RCOR1	chr4:119199529-119200285	K562	blood:	n/a	n/a
46	TAF1	chr4:119199458-119200430	K562	blood:	n/a	n/a
47	NRF1	chr4:119199086-119200330	SK-N-SH	brain:	n/a	chr4:119199690-119199699 chr4:119199690-119199701 chr4:119199689-119199700 chr4:119199687-119199701
48	JUND	chr4:119199452-119203796	SK-N-SH	brain:	n/a	chr4:119199812-119199821 chr4:119203525-119203535
49	RFX5	chr4:119199564-119200370	HepG2	liver:	n/a	chr4:119199873-119199881
50	GATA1	chr4:119199678-119201029	PBDE	blood:	n/a	chr4:119200705-119200721 chr4:119200708-119200717

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:119199871-119199921	SAEC	small airway:	n/a
2	chr4:119199871-119199921	GM12891	blood:	n/a
3	chr4:119199871-119199921	ECC-1	luminal epithelium:	n/a
4	chr4:119199842-119199892	GM12891	blood:	n/a
5	chr4:119199842-119199892	HCF	heart:	n/a
6	chr4:119199842-119199892	HL-60	blood:	n/a
7	chr4:119199871-119199921	HEEpiC	esophagus:	n/a
8	chr4:119199871-119199921	HMEC	breast:	n/a
9	chr4:119199871-119199921	NHBE	bronchial:	n/a
10	chr4:119199842-119199892	ovcar-3	ovarian:	n/a
11	chr4:119199871-119199921	HL-60	blood:	n/a
12	chr4:119199842-119199892	HRE	kidney:	n/a
13	chr4:119199871-119199921	AoSMC	blood vessel:	n/a
14	chr4:119199871-119199921	BE2_C	brain:	n/a
15	chr4:119199842-119199892	GM12892	blood:	n/a
16	chr4:119199842-119199892	U87	brain:	n/a
17	chr4:119199842-119199892	HEEpiC	esophagus:	n/a
18	chr4:119199842-119199892	HMEC	breast:	n/a
19	chr4:119199871-119199921	CMK	blood:	n/a
20	chr4:119199871-119199921	AG04449	skin:	fetal
21	chr4:119199842-119199892	HRPEpiC	eye:	n/a
22	chr4:119199871-119199921	Hepatocyte	liver:	n/a
23	chr4:119199871-119199921	SK-N-SH	brain:	n/a
24	chr4:119199842-119199892	AG09319	gingival:	n/a
25	chr4:119199871-119199921	HCT-116	colon:	n/a
26	chr4:119199842-119199892	PrEC	prostate:	n/a
27	chr4:119199842-119199892	HCM	heart:	n/a
28	chr4:119199842-119199892	HAEpiC	amniotic membrane:	n/a
29	chr4:119199842-119199892	AG04449	skin:	fetal
30	chr4:119199871-119199921	LNCaP	prostate:	n/a
31	chr4:119199871-119199921	HEK293	kidney:	embryo
32	chr4:119199871-119199921	RPTEC	kidney:	n/a
33	chr4:119199842-119199892	PFSK-1	brain:	n/a
34	chr4:119199871-119199921	HCM	heart:	n/a
35	chr4:119199871-119199921	NT2-D1	testis:	n/a
36	chr4:119199842-119199892	Jurkat	blood:	n/a
37	chr4:119199842-119199892	HCT-116	colon:	n/a
38	chr4:119199871-119199921	Hela-S3	cervix:	n/a
39	chr4:119199842-119199892	CMK	blood:	n/a
40	chr4:119199871-119199921	AG10803	skin:	n/a
41	chr4:119199842-119199892	SK-N-MC	brain:	n/a
42	chr4:119199871-119199921	HRCEpiC	kidney:	n/a
43	chr4:119199842-119199892	T-47D	breast:	n/a
44	chr4:119199842-119199892	NT2-D1	testis:	n/a
45	chr4:119199842-119199892	BJ	skin:	n/a
46	chr4:119199871-119199921	GM12878	blood:	n/a
47	chr4:119199871-119199921	PrEC	prostate:	n/a
48	chr4:119199842-119199892	ProgFib	skin:	n/a
49	chr4:119199842-119199892	SKMC	muscle:	n/a
50	chr4:119199842-119199892	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:119198265..119200504-chr4:119654029..119656125,2	K562	blood:
2	chr4:119198319..119200411-chr6:26198105..26199834,2	MCF-7	breast:
3	chr4:119199845..119203643-chr4:119232853..119237501,6	K562	blood:
4	chr4:119198442..119201160-chr4:120987880..120989467,2	MCF-7	breast:
5	chr16:9185065..9185987-chr4:119199511..119200039,2	Hela-S3	cervix:
6	chr4:119199692..119204423-chr4:119272219..119275323,9	MCF-7	breast:
7	chr4:119199785..119200370-chr8:94752741..94753419,2	HCT-116	colon:
8	chr12:80084545..80085382-chr4:119199795..119200450,2	Hela-S3	cervix:
9	chr4:119199307..119202288-chr4:119603050..119607934,6	MCF-7	breast:
10	chr4:119198677..119205956-chr4:119272273..119279963,18	MCF-7	breast:
11	chr4:119199772..119200721-chrX:100662278..100663232,2	Hela-S3	cervix:
12	chr18:12991026..12991868-chr4:119199244..119200267,3	Hela-S3	cervix:
13	chr17:39942474..39943145-chr4:119199596..119200272,2	Hela-S3	cervix:

Variant related genes	Relation type
SNHG8	TF binding region
SNHG8	CpG island
ENSG00000250938	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000164099	Chromatin interaction
ENSG00000102393	Chromatin interaction
ENSG00000150961	Chromatin interaction
ENSG00000145388	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000177425	Chromatin interaction
ENSG00000182831	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000173801	Chromatin interaction
ENSG00000183808	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000197409	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11929737	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs11933355	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs11935046	0.87[AFR][1000 genomes]
rs34131974	0.96[AFR][1000 genomes]
rs34548184	0.81[EUR][1000 genomes]
rs71608362	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71608364	0.86[EUR][1000 genomes]
rs7670243	0.96[AFR][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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1003731	chr4:119138262-119506032	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv1794655	chr4:119170156-119212103	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7678308	SNHG8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119197800-119200800	Active TSS	Duodenum Mucosa	Duodenum
2	chr4:119198200-119200200	Active TSS	GM12878-XiMat	blood
3	chr4:119198600-119201000	Active TSS	Liver	Liver
4	chr4:119198800-119200200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:119198800-119200200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:119198800-119200400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:119198800-119200400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr4:119198800-119200400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:119198800-119200400	Active TSS	K562	blood
10	chr4:119198800-119200600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:119198800-119200600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:119198800-119200600	Active TSS	NH-A	brain
13	chr4:119199000-119200000	Active TSS	HepG2	liver
14	chr4:119199000-119200200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:119199000-119200200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr4:119199000-119200200	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr4:119199000-119200200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr4:119199000-119200400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:119199000-119200400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:119199000-119200400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:119199000-119200400	Active TSS	Fetal Brain Male	brain
22	chr4:119199000-119200400	Active TSS	HMEC	breast
23	chr4:119199000-119200400	Active TSS	Osteobl	bone
24	chr4:119199000-119200600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr4:119199000-119200600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:119199000-119200600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:119199000-119200600	Active TSS	Brain Anterior Caudate	brain
28	chr4:119199000-119200600	Active TSS	Brain Hippocampus Middle	brain
29	chr4:119199000-119200600	Active TSS	Fetal Brain Female	brain
30	chr4:119199000-119200600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:119199000-119200600	Active TSS	Hela-S3	cervix
32	chr4:119199000-119200800	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr4:119199000-119200800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:119199000-119200800	Active TSS	Colon Smooth Muscle	Colon
35	chr4:119199000-119200800	Active TSS	NHLF	lung
36	chr4:119199000-119201000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:119199000-119201000	Active TSS	Aorta	Aorta
38	chr4:119199000-119201000	Active TSS	Placenta	Placenta
39	chr4:119199000-119201000	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr4:119199000-119201000	Active TSS	Stomach Mucosa	stomach
41	chr4:119199000-119201200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr4:119199000-119201200	Active TSS	Brain Angular Gyrus	brain
43	chr4:119199000-119201200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr4:119199000-119201200	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr4:119199000-119201200	Active TSS	Fetal Kidney	kidney
46	chr4:119199000-119201400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:119199000-119201400	Active TSS	Rectal Smooth Muscle	rectum
48	chr4:119199000-119201600	Active TSS	Colonic Mucosa	Colon
49	chr4:119199000-119201600	Active TSS	Psoas Muscle	Psoas
50	chr4:119199000-119202000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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