Variant report

Variant	rs1523742
Chromosome Location	chr4:119199053-119199054
allele	A/C
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	POLR2A	chr4:119197988-119206014	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:119198979-119204800	PBDE	blood:	n/a	n/a
3	TBL1XR1	chr4:119199032-119200403	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:119198968-119204881	K562	blood:	n/a	n/a
5	IRF1	chr4:119198889-119203207	K562	blood:	n/a	chr4:119199812-119199826 chr4:119198955-119198966 chr4:119198952-119198965 chr4:119200643-119200660 chr4:119199835-119199849
6	RELA	chr4:119198729-119200786	GM18505	blood:	n/a	n/a
7	STAT3	chr4:119198996-119199233	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr4:119198411-119204666	SK-N-SH	brain:	n/a	n/a
9	MYC	chr4:119198887-119199270	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr4:119199010-119204847	GM19099	blood:	n/a	n/a
11	POLR2A	chr4:119198623-119205724	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr4:119198552-119205767	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr4:119198541-119204580	GM18505	blood:	n/a	n/a
14	POLR2A	chr4:119199034-119204440	GM12892	blood:	n/a	n/a
15	IRF1	chr4:119199022-119202560	K562	blood:	n/a	chr4:119199812-119199826 chr4:119200643-119200660 chr4:119199835-119199849
16	CEBPB	chr4:119198807-119200677	GM12878	blood:	n/a	n/a
17	TBP	chr4:119198813-119201130	GM12878	blood:	n/a	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	chr4:119150653..119153442-chr4:119197486..119199123,2	K562	blood:
4	chr4:119198442..119201160-chr4:120987880..120989467,2	MCF-7	breast:
5	chr4:119198677..119205956-chr4:119272273..119279963,18	MCF-7	breast:

Variant related genes	Relation type
SNHG8	TF binding region
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000164099	Chromatin interaction
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11098432	0.80[JPT][hapmap]
rs11098433	0.91[CEU][hapmap]
rs13120959	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2030635	0.82[EUR][1000 genomes]
rs2389618	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28517808	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3107483	0.87[GIH][hapmap]
rs3805189	0.85[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs3828500	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs4833571	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582448	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs586073	0.85[YRI][hapmap]
rs617140	0.86[YRI][hapmap]
rs627249	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs631271	0.87[GIH][hapmap]
rs7697292	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs788655	0.85[YRI][hapmap]
rs788662	0.86[YRI][hapmap]
rs788663	0.87[GIH][hapmap]
rs788668	0.86[YRI][hapmap]
rs883686	0.89[CEU][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]

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
rs1523742	SNHG8	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119187200-119199400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:119197600-119199200	Weak transcription	Pancreas	Pancrea
3	chr4:119197600-119199400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:119197800-119200800	Active TSS	Duodenum Mucosa	Duodenum
5	chr4:119198200-119200200	Active TSS	GM12878-XiMat	blood
6	chr4:119198400-119199200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:119198400-119199200	Enhancers	Fetal Thymus	thymus
8	chr4:119198400-119199400	Flanking Active TSS	Fetal Intestine Large	intestine
9	chr4:119198600-119199200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:119198600-119199400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:119198600-119201000	Active TSS	Liver	Liver
12	chr4:119198800-119199200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:119198800-119199200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:119198800-119199200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:119198800-119199400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr4:119198800-119199400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr4:119198800-119199400	Flanking Active TSS	NHEK	skin
18	chr4:119198800-119199600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:119198800-119200200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr4:119198800-119200200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:119198800-119200400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr4:119198800-119200400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr4:119198800-119200400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:119198800-119200400	Active TSS	K562	blood
25	chr4:119198800-119200600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:119198800-119200600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr4:119198800-119200600	Active TSS	NH-A	brain
28	chr4:119199000-119199200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr4:119199000-119199200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr4:119199000-119199200	Enhancers	Primary T cells from cord blood	blood
31	chr4:119199000-119199200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr4:119199000-119199200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:119199000-119199200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:119199000-119199200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr4:119199000-119199200	Enhancers	Brain Substantia Nigra	brain
36	chr4:119199000-119199200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:119199000-119199200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr4:119199000-119199200	Active TSS	Stomach Smooth Muscle	stomach
39	chr4:119199000-119199200	Flanking Active TSS	A549	lung
40	chr4:119199000-119199200	Enhancers	NHDF-Ad	bronchial
41	chr4:119199000-119199400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:119199000-119199400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr4:119199000-119199400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr4:119199000-119199400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:119199000-119199400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr4:119199000-119199400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr4:119199000-119199400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:119199000-119199400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr4:119199000-119199400	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr4:119199000-119199400	Enhancers	Fetal Heart	heart

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