Variant report

Variant	rs11098940
Chromosome Location	chr4:128778486-128778487
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128777977..128780452-chr4:128800895..128803398,3	K562	blood:

Variant related genes	Relation type
ENSG00000142731	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10857126	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11098936	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs11725843	0.88[EUR][1000 genomes]
rs11735635	0.91[CEU][hapmap]
rs12503257	0.84[EUR][1000 genomes]
rs12504266	0.87[CEU][hapmap]
rs12504825	0.91[CEU][hapmap]
rs12511932	0.91[CEU][hapmap]
rs12645068	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12645636	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs13127610	0.82[CEU][hapmap]
rs1380156	0.91[CEU][hapmap]
rs1459048	0.82[CEU][hapmap]
rs1459050	0.91[CEU][hapmap]
rs1585311	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1585312	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17012739	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1870422	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1903104	0.82[CEU][hapmap]
rs2087446	0.84[EUR][1000 genomes]
rs2305957	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2305958	0.91[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34625382	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3775982	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3811740	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs3816588	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs4435753	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs4833391	0.82[CEU][hapmap]
rs4834217	0.82[CEU][hapmap]
rs4834223	0.96[CEU][hapmap]
rs55798529	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335590	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534638	0.83[CEU][hapmap]
rs6534647	0.88[EUR][1000 genomes]
rs6534648	0.91[CEU][hapmap]
rs6534655	0.83[EUR][1000 genomes]
rs6839292	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7376138	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs748630	0.87[CEU][hapmap]
rs7654638	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs7671590	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7684368	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7692740	0.87[CEU][hapmap]
rs769293	0.82[CEU][hapmap]
rs959822	0.86[CEU][hapmap]
rs9968459	0.91[CEU][hapmap]
rs9995738	0.91[CEU][hapmap];0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv830057	chr4:128591288-128788777	Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128774200-128779600	Weak transcription	Primary T cells from cord blood	blood
2	chr4:128774200-128779600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:128776600-128782200	Weak transcription	Dnd41	blood
4	chr4:128777000-128779600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr4:128777200-128778600	Enhancers	Fetal Heart	heart
6	chr4:128777200-128779200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:128777400-128778600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr4:128777400-128778600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:128777400-128778600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:128777400-128778600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:128777400-128778600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:128777400-128778600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr4:128777400-128778600	Enhancers	HSMM	muscle
14	chr4:128777400-128779000	Flanking Active TSS	GM12878-XiMat	blood
15	chr4:128777400-128779000	Enhancers	Osteobl	bone
16	chr4:128777600-128778600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:128777600-128778600	Enhancers	NHLF	lung
18	chr4:128777600-128778800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr4:128777800-128778600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:128777800-128778600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:128777800-128778600	Enhancers	Duodenum Mucosa	Duodenum
22	chr4:128777800-128778800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr4:128777800-128779000	Enhancers	NHDF-Ad	bronchial
24	chr4:128777800-128779200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:128778000-128778600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:128778000-128778600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:128778000-128778600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:128778000-128778600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:128778000-128778600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:128778000-128778600	Enhancers	Lung	lung
31	chr4:128778000-128778600	Enhancers	HSMMtube	muscle
32	chr4:128778000-128778600	Flanking Active TSS	NH-A	brain
33	chr4:128778000-128778600	Flanking Active TSS	NHEK	skin
34	chr4:128778000-128778800	Enhancers	HepG2	liver
35	chr4:128778000-128778800	Flanking Active TSS	HMEC	breast
36	chr4:128778000-128779200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:128778000-128779200	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr4:128778200-128778600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:128778200-128778600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:128778200-128778800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:128778200-128779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:128778200-128779600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:128778400-128778600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:128778400-128778600	Active TSS	Adipose Nuclei	Adipose
45	chr4:128778400-128780200	Weak transcription	Primary B cells from peripheral blood	blood

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