Variant report

Variant	rs41335053
Chromosome Location	chr4:56995602-56995603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56995303..56996217-chr4:57702535..57703041,2	MCF-7	breast:
2	chr4:56994960..56996210-chr4:57167032..57168215,14	MCF-7	breast:
3	chr4:56995263..56996196-chr4:57049303..57050160,2	K562	blood:
4	chr4:56995235..56996245-chr4:57167093..57168027,4	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10008254	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs10030394	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11723545	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731420	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11736354	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2127198	0.80[ASN][1000 genomes]
rs28392731	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28407980	0.82[ASN][1000 genomes]
rs28418386	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28421026	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28433043	0.93[ASN][1000 genomes]
rs28463663	0.82[ASN][1000 genomes]
rs28603237	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554333	0.82[ASN][1000 genomes]
rs7686487	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv999328	chr4:56942917-57041586	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1007114	chr4:56942917-57055381	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1012036	chr4:56963544-57106642	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56952000-57024400	Weak transcription	Fetal Intestine Small	intestine
2	chr4:56993000-57000400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:56993200-56996200	Enhancers	Fetal Stomach	stomach
4	chr4:56993200-56996400	Enhancers	Brain Germinal Matrix	brain
5	chr4:56993200-56997800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:56993800-56997400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:56993800-56997800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:56994000-57000400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:56994200-57000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:56994200-57000400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:56994400-56995800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:56994400-56995800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:56994400-56999800	Weak transcription	Hela-S3	cervix
14	chr4:56994400-57000000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:56994400-57000200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:56994400-57000400	Weak transcription	NH-A	brain
17	chr4:56994400-57003000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:56994400-57015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:56994600-56995800	Weak transcription	Fetal Lung	lung
20	chr4:56994600-56996600	Weak transcription	HUVEC	blood vessel
21	chr4:56994600-56997000	Weak transcription	Fetal Kidney	kidney
22	chr4:56994600-57001600	Weak transcription	Fetal Brain Female	brain
23	chr4:56994800-57000000	Weak transcription	HSMM	muscle
24	chr4:56994800-57000200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:56994800-57000200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:56995000-56996800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:56995000-57000200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:56995000-57000400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:56995400-56997200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:56995600-56996000	Enhancers	Fetal Brain Male	brain
31	chr4:56995600-56996200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr4:56995600-56996200	Enhancers	HepG2	liver
33	chr4:56995600-56999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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