Variant report

Variant	rs4234985
Chromosome Location	chr4:27124660-27124661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:27123166..27125780-chr4:27126657..27128387,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11727911	0.83[EUR][1000 genomes]
rs12503097	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13108236	0.83[EUR][1000 genomes]
rs13113425	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35241736	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35281978	0.84[EUR][1000 genomes]
rs36084087	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55833139	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844289	0.81[EUR][1000 genomes]
rs741130	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs741137	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs757632	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759113	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7696691	0.83[EUR][1000 genomes];0.84[ASN][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	nsv1002082	chr4:27078850-27377252	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv997608	chr4:27085524-27371848	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv999134	chr4:27115301-27270500	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4234985	SEL1L3	cis	parietal	SCAN
rs4234985	ZCCHC4	cis	parietal	SCAN
rs4234985	SOD3	cis	cerebellum	SCAN
rs4234985	SLC34A2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:27122600-27125600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:27122600-27125800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:27122600-27126600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:27122800-27125600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:27122800-27126800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:27122800-27126800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:27122800-27127200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:27123000-27126000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:27123000-27126400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr4:27123000-27127000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:27123200-27125000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:27123600-27126600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr4:27123800-27126600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:27123800-27126600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:27124200-27124800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr4:27124200-27125800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:27124200-27126000	Enhancers	Fetal Intestine Large	intestine
18	chr4:27124400-27124800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:27124400-27124800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr4:27124400-27124800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr4:27124400-27125200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr4:27124400-27125200	Enhancers	Colonic Mucosa	Colon
23	chr4:27124600-27124800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr4:27124600-27124800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr4:27124600-27124800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr4:27124600-27125600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:27124600-27125600	Enhancers	Fetal Intestine Small	intestine
28	chr4:27124600-27125600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr4:27124600-27125800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:27124600-27125800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:27124600-27129000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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