Variant report

Variant	rs11935039
Chromosome Location	chr4:95380012-95380013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95377886..95380417-chr4:95453413..95456083,2	K562	blood:
2	chr4:95378587..95381661-chr4:95382526..95385880,5	K562	blood:
3	chr4:95379639..95382312-chr4:95516678..95518762,3	K562	blood:
4	chr4:95377004..95378631-chr4:95378728..95380869,2	MCF-7	breast:
5	chr4:95371672..95374851-chr4:95376259..95380143,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203436	Chromatin interaction
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11097429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11097430	0.91[AMR][1000 genomes]
rs11932136	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11932224	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11933735	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935012	0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935084	0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11935947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11939756	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11940613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941259	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941353	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11942920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11946663	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56827347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58528979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6845473	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874705	1.00[EUR][1000 genomes]
rs72874730	1.00[EUR][1000 genomes]
rs72874733	1.00[EUR][1000 genomes]
rs72874739	1.00[EUR][1000 genomes]
rs72874745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874752	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874760	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874764	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874769	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874781	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874802	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876211	1.00[EUR][1000 genomes]
rs72876216	1.00[EUR][1000 genomes]
rs72876217	1.00[EUR][1000 genomes]
rs72876219	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876229	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876241	1.00[EUR][1000 genomes]
rs72890408	1.00[EUR][1000 genomes]
rs72890416	1.00[EUR][1000 genomes]
rs7673478	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95374200-95387000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:95374200-95388600	Weak transcription	Gastric	stomach
3	chr4:95374200-95389200	Weak transcription	Lung	lung
4	chr4:95374200-95395400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:95374200-95400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:95374400-95382400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:95374600-95380200	Weak transcription	Primary B cells from cord blood	blood
8	chr4:95374600-95381000	Weak transcription	Spleen	Spleen
9	chr4:95374600-95382200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:95374600-95388800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:95374800-95380600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:95374800-95381600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:95374800-95385200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:95374800-95398200	Weak transcription	Esophagus	oesophagus
15	chr4:95375000-95380600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:95375000-95380600	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr4:95375000-95387600	Weak transcription	Fetal Stomach	stomach
18	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
19	chr4:95375800-95401600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:95376000-95380800	Weak transcription	Colonic Mucosa	Colon
21	chr4:95376000-95385000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:95376600-95381200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:95376600-95392000	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:95376800-95380200	Genic enhancers	NHEK	skin
25	chr4:95377000-95381800	Genic enhancers	HepG2	liver
26	chr4:95377200-95380800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:95377200-95382200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:95377800-95382600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:95378000-95380200	Genic enhancers	HSMM	muscle
30	chr4:95378000-95380600	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr4:95378000-95383000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:95378200-95380800	Weak transcription	Left Ventricle	heart
33	chr4:95378200-95383200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:95378400-95381200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:95378400-95381800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:95378400-95382600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:95378400-95383600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr4:95378600-95380800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:95378800-95380200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:95378800-95380400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:95378800-95381000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:95378800-95381000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:95378800-95381200	Enhancers	Brain Angular Gyrus	brain
44	chr4:95378800-95381400	Enhancers	Colon Smooth Muscle	Colon
45	chr4:95378800-95382800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:95378800-95383000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr4:95378800-95384200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr4:95378800-95391200	Weak transcription	Placenta	Placenta
49	chr4:95379000-95380600	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr4:95379000-95381000	Enhancers	Stomach Mucosa	stomach

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