Variant report

Variant	rs6554399
Chromosome Location	chr4:57792991-57792992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57775317..57777914-chr4:57791258..57794432,4	K562	blood:
2	chr4:57775317..57777346-chr4:57791863..57794432,2	K562	blood:
3	chr4:57774089..57775634-chr4:57791349..57793300,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10030913	0.83[ASN][1000 genomes]
rs10866440	0.83[ASN][1000 genomes]
rs10866441	0.86[ASN][1000 genomes]
rs1105434	0.89[ASN][1000 genomes]
rs1107675	0.89[ASN][1000 genomes]
rs11729152	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11730525	0.81[ASN][1000 genomes]
rs11736192	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11736808	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736869	0.91[ASN][1000 genomes]
rs11736965	0.88[ASN][1000 genomes]
rs11737689	0.84[ASN][1000 genomes]
rs11932673	0.90[ASN][1000 genomes]
rs11933908	0.81[ASN][1000 genomes]
rs12500454	0.89[ASN][1000 genomes]
rs12501224	0.86[ASN][1000 genomes]
rs12501990	0.89[ASN][1000 genomes]
rs12502076	0.85[ASN][1000 genomes]
rs1277271	0.87[ASN][1000 genomes]
rs13108245	0.81[ASN][1000 genomes]
rs13113802	0.82[ASN][1000 genomes]
rs13121176	0.85[ASN][1000 genomes]
rs13131605	0.84[ASN][1000 genomes]
rs13136432	0.86[ASN][1000 genomes]
rs13146960	0.81[ASN][1000 genomes]
rs13149162	0.80[ASN][1000 genomes]
rs13150593	0.86[ASN][1000 genomes]
rs13152476	0.85[ASN][1000 genomes]
rs17087307	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17087317	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1718839	0.88[ASN][1000 genomes]
rs1877669	0.81[ASN][1000 genomes]
rs1963666	0.81[ASN][1000 genomes]
rs1976780	0.90[ASN][1000 genomes]
rs2014870	0.84[ASN][1000 genomes]
rs2228991	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000	0.81[ASN][1000 genomes]
rs34124552	0.86[ASN][1000 genomes]
rs34448457	0.86[ASN][1000 genomes]
rs34576794	0.85[ASN][1000 genomes]
rs34659774	0.90[ASN][1000 genomes]
rs35267092	0.86[ASN][1000 genomes]
rs3733306	0.84[ASN][1000 genomes]
rs3796528	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806745	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4864606	0.81[ASN][1000 genomes]
rs4864607	0.80[ASN][1000 genomes]
rs4864608	0.89[ASN][1000 genomes]
rs62308135	0.81[ASN][1000 genomes]
rs62308136	0.81[ASN][1000 genomes]
rs62308137	0.80[ASN][1000 genomes]
rs62308155	0.85[ASN][1000 genomes]
rs6554397	0.81[ASN][1000 genomes]
rs6554398	0.83[ASN][1000 genomes]
rs6816457	0.87[ASN][1000 genomes]
rs6838948	0.81[ASN][1000 genomes]
rs6852110	0.89[ASN][1000 genomes]
rs6854420	0.81[ASN][1000 genomes]
rs73242609	0.81[ASN][1000 genomes]
rs73242616	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73242617	0.81[EUR][1000 genomes]
rs7680734	0.89[ASN][1000 genomes]
rs7685576	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695970	0.81[ASN][1000 genomes]
rs781665	0.88[ASN][1000 genomes]
rs781666	0.88[ASN][1000 genomes]
rs781668	0.88[ASN][1000 genomes]
rs9942208	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1797793	chr4:57786450-57793425	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57777000-57795800	Weak transcription	A549	lung
2	chr4:57777000-57796600	Weak transcription	Fetal Brain Female	brain
3	chr4:57777000-57797000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:57777200-57793400	Weak transcription	HMEC	breast
5	chr4:57777200-57796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:57777200-57796600	Weak transcription	Aorta	Aorta
7	chr4:57777200-57796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:57777200-57797200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:57777600-57796000	Weak transcription	Brain Anterior Caudate	brain
10	chr4:57777600-57796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:57777600-57796600	Weak transcription	Colonic Mucosa	Colon
12	chr4:57777600-57803200	Weak transcription	NHDF-Ad	bronchial
13	chr4:57777600-57805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:57777600-57806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:57778000-57796000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:57778000-57796000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:57778000-57796600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:57778000-57797000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:57778200-57796200	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:57778200-57796800	Weak transcription	NHLF	lung
21	chr4:57778400-57795400	Weak transcription	HSMMtube	muscle
22	chr4:57778400-57796000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:57778400-57800200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:57778400-57800200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:57778400-57801000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:57778800-57795800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:57779000-57804600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:57779200-57799200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:57779800-57796000	Weak transcription	Small Intestine	intestine
30	chr4:57779800-57797600	Weak transcription	Fetal Brain Male	brain
31	chr4:57779800-57799600	Weak transcription	Right Atrium	heart
32	chr4:57780200-57793000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:57780400-57800400	Strong transcription	Fetal Thymus	thymus
34	chr4:57780800-57795600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:57780800-57808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:57781000-57796800	Weak transcription	Spleen	Spleen
37	chr4:57781000-57799600	Weak transcription	Psoas Muscle	Psoas
38	chr4:57781800-57801400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:57782400-57796000	Weak transcription	Hela-S3	cervix
40	chr4:57782800-57796800	Weak transcription	Pancreas	Pancrea
41	chr4:57783000-57798400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:57783200-57796200	Weak transcription	Fetal Heart	heart
43	chr4:57783200-57801400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:57783800-57796400	Weak transcription	Brain Substantia Nigra	brain
45	chr4:57783800-57802000	Strong transcription	Dnd41	blood
46	chr4:57784200-57800000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr4:57784800-57798200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:57785200-57796800	Weak transcription	Gastric	stomach
49	chr4:57785400-57800800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr4:57785800-57793000	Strong transcription	Fetal Lung	lung

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