Variant report

Variant	rs11098433
Chromosome Location	chr4:119246541-119246542
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119199843..119203968-chr4:119245801..119250116,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269893	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13120959	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1523742	0.91[CEU][hapmap]
rs2030635	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2292597	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2389618	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs3107483	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs3805189	0.87[CEU][hapmap]
rs4833571	0.91[CEU][hapmap]
rs623035	0.86[JPT][hapmap]
rs631271	0.92[CHB][hapmap]
rs658642	0.84[JPT][hapmap]
rs705837	0.86[JPT][hapmap]
rs7697292	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs788663	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs883686	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs972814	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv3408889	chr4:119243370-119247305	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3467350	chr4:119243552-119247153	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3467351	chr4:119243584-119247192	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3467349	chr4:119243619-119247182	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv3467353	chr4:119243714-119247081	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11098433	SNHG8	cis	Muscle Skeletal	GTEx
rs11098433	SNHG8	cis	Heart Left Ventricle	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119202800-119267200	Weak transcription	Stomach Mucosa	stomach
2	chr4:119209600-119258600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:119210000-119259200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:119210200-119258600	Weak transcription	HMEC	breast
5	chr4:119212600-119259200	Weak transcription	NHEK	skin
6	chr4:119216400-119249800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:119220200-119260000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:119229000-119267200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:119233000-119246600	Weak transcription	Fetal Stomach	stomach
10	chr4:119237600-119250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:119239800-119259200	Weak transcription	Fetal Brain Male	brain
12	chr4:119240800-119246600	Weak transcription	NHLF	lung
13	chr4:119241200-119248800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:119243800-119252800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:119243800-119259000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:119244400-119246600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:119244400-119246600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:119244400-119246800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:119244600-119246600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:119244600-119246600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:119244800-119248600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:119244800-119248600	Weak transcription	Osteobl	bone
23	chr4:119245200-119246800	Weak transcription	Fetal Lung	lung
24	chr4:119245600-119247200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr4:119246200-119247200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:119246200-119247600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:119246200-119250400	Enhancers	NHDF-Ad	bronchial
28	chr4:119246400-119246800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:119246400-119250000	Weak transcription	Fetal Muscle Trunk	muscle

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