Variant report

Variant	rs623035
Chromosome Location	chr4:119204851-119204852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:119203107..119204867-chr4:119240756..119242406,2	K562	blood:
2	chr4:119203891..119206075-chr4:119600077..119602482,2	K562	blood:
3	chr4:119202799..119206241-chr4:119218807..119222777,4	MCF-7	breast:
4	chr4:119200823..119205436-chr4:119252231..119259407,8	K562	blood:
5	chr4:119203054..119205344-chr4:119252768..119255256,2	MCF-7	breast:
6	chr4:119204030..119205775-chr4:119295374..119296879,2	K562	blood:
7	chr4:119203588..119205847-chr4:119243222..119244861,2	MCF-7	breast:
8	chr4:119198677..119205956-chr4:119272273..119279963,18	MCF-7	breast:
9	chr4:119202174..119205868-chr4:119258505..119262976,4	MCF-7	breast:
10	chr4:119203944..119207755-chr4:119250346..119253066,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164099	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11098433	0.86[JPT][hapmap]
rs12506555	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12509230	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17626497	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2389618	0.80[CEU][hapmap]
rs3107483	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35159999	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35789417	0.89[EUR][1000 genomes]
rs55747202	0.86[EUR][1000 genomes]
rs609512	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs611659	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs615517	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs617430	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs631271	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs633398	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs640713	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs658642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662581	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs673682	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs687492	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs705837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs788646	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs788649	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs788663	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs788666	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs623035	SNHG8	cis	Skin Sun Exposed Lower leg	GTEx
rs623035	SNHG8	cis	Thyroid	GTEx
rs623035	SNHG8	cis	Muscle Skeletal	GTEx
rs623035	SNHG8	cis	Heart Left Ventricle	GTEx

Chromatin state (count:77 , 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	chr4:119201000-119205600	Weak transcription	Aorta	Aorta
3	chr4:119201400-119205400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:119201400-119206200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:119201400-119207400	Weak transcription	Esophagus	oesophagus
6	chr4:119201400-119216200	Weak transcription	Lung	lung
7	chr4:119201400-119223800	Weak transcription	Gastric	stomach
8	chr4:119201800-119205200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr4:119202000-119205400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:119202200-119205400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:119202200-119205600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:119202200-119205800	Enhancers	Liver	Liver
13	chr4:119202200-119208800	Weak transcription	Thymus	Thymus
14	chr4:119202200-119209400	Weak transcription	Fetal Stomach	stomach
15	chr4:119202200-119210800	Weak transcription	Brain Angular Gyrus	brain
16	chr4:119202200-119211600	Weak transcription	Brain Germinal Matrix	brain
17	chr4:119202200-119225000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:119202400-119206000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:119202400-119220800	Weak transcription	Fetal Brain Female	brain
20	chr4:119202600-119205200	Strong transcription	Primary B cells from cord blood	blood
21	chr4:119202600-119205200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:119202600-119205400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:119202600-119205600	Strong transcription	Fetal Thymus	thymus
24	chr4:119202600-119207000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:119202600-119207000	Weak transcription	Psoas Muscle	Psoas
26	chr4:119202600-119207200	Weak transcription	Right Ventricle	heart
27	chr4:119202800-119205600	Weak transcription	Dnd41	blood
28	chr4:119202800-119206000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:119202800-119267200	Weak transcription	Stomach Mucosa	stomach
30	chr4:119203000-119210600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:119203200-119205200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:119203400-119205200	Weak transcription	Ovary	ovary
33	chr4:119203400-119205400	Weak transcription	Adipose Nuclei	Adipose
34	chr4:119203400-119205600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:119203400-119205600	Weak transcription	Fetal Intestine Small	intestine
36	chr4:119203400-119207200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:119203400-119207600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:119203400-119208400	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:119203400-119212400	Weak transcription	Left Ventricle	heart
40	chr4:119203400-119228200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:119203600-119205800	Enhancers	K562	blood
42	chr4:119203600-119208200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:119203600-119209000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:119203600-119210000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr4:119203800-119205600	Strong transcription	Primary T cells from cord blood	blood
46	chr4:119203800-119205600	Weak transcription	A549	lung
47	chr4:119203800-119206000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:119204000-119205200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:119204000-119205400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:119204000-119205400	Weak transcription	NHLF	lung

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