Variant report

Variant	rs4834677
Chromosome Location	chr4:119205878-119205879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119203891..119206075-chr4:119600077..119602482,2	K562	blood:
2	chr4:119202799..119206241-chr4:119218807..119222777,4	MCF-7	breast:
3	chr4:119205014..119207897-chr4:119243255..119244938,2	K562	blood:
4	chr4:119198677..119205956-chr4:119272273..119279963,18	MCF-7	breast:
5	chr4:119203944..119207755-chr4:119250346..119253066,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164099	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10030445	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098432	0.81[ASN][1000 genomes]
rs11947394	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13132331	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13145025	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642201	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949760	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2138009	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389567	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620219	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892800	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34399419	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34913869	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805189	0.80[ASN][1000 genomes]
rs3828500	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4327555	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833570	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833572	0.81[AFR][1000 genomes]
rs4834670	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4834672	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834675	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834678	0.82[AFR][1000 genomes]
rs6825871	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674426	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690554	0.81[AFR][1000 genomes]
rs9685810	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972813	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9884481	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4834677	SNHG8	Cis_1M	lymphoblastoid	RTeQTL
rs4834677	SNHG8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119200800-119212800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:119201400-119206200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:119201400-119207400	Weak transcription	Esophagus	oesophagus
4	chr4:119201400-119216200	Weak transcription	Lung	lung
5	chr4:119201400-119223800	Weak transcription	Gastric	stomach
6	chr4:119202200-119208800	Weak transcription	Thymus	Thymus
7	chr4:119202200-119209400	Weak transcription	Fetal Stomach	stomach
8	chr4:119202200-119210800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:119202200-119211600	Weak transcription	Brain Germinal Matrix	brain
10	chr4:119202200-119225000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:119202400-119206000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:119202400-119220800	Weak transcription	Fetal Brain Female	brain
13	chr4:119202600-119207000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:119202600-119207000	Weak transcription	Psoas Muscle	Psoas
15	chr4:119202600-119207200	Weak transcription	Right Ventricle	heart
16	chr4:119202800-119206000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:119202800-119267200	Weak transcription	Stomach Mucosa	stomach
18	chr4:119203000-119210600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:119203400-119207200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:119203400-119207600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:119203400-119208400	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:119203400-119212400	Weak transcription	Left Ventricle	heart
23	chr4:119203400-119228200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:119203600-119208200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:119203600-119209000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:119203600-119210000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:119203800-119206000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:119204000-119206200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:119204000-119208600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:119204000-119210800	Weak transcription	NH-A	brain
31	chr4:119204200-119206600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:119204200-119207600	Weak transcription	Fetal Lung	lung
33	chr4:119204400-119206000	Weak transcription	Brain Anterior Caudate	brain
34	chr4:119204400-119206000	Weak transcription	Fetal Intestine Large	intestine
35	chr4:119204400-119208200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:119204600-119206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:119204600-119206400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr4:119204600-119206600	Weak transcription	HMEC	breast
39	chr4:119204600-119208000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:119204800-119206000	Enhancers	GM12878-XiMat	blood
41	chr4:119204800-119207200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:119204800-119208200	Weak transcription	Osteobl	bone
43	chr4:119204800-119208800	Weak transcription	NHDF-Ad	bronchial
44	chr4:119204800-119209000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:119204800-119209000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:119205000-119207200	Enhancers	NHEK	skin
47	chr4:119205200-119206000	Genic enhancers	Primary B cells from cord blood	blood
48	chr4:119205200-119206000	Enhancers	Primary B cells from peripheral blood	blood
49	chr4:119205400-119206000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:119205400-119206000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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