Variant report

Variant	rs6845250
Chromosome Location	chr4:48486193-48486194
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	chr4:48484114..48487251-chr4:48504187..48509460,5	K562	blood:
2	chr4:48485954..48488857-chr4:48528912..48531083,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10517218	0.89[EUR][1000 genomes]
rs10805169	0.95[EUR][1000 genomes]
rs13102023	0.89[EUR][1000 genomes]
rs13105648	0.90[EUR][1000 genomes]
rs13110633	0.88[EUR][1000 genomes]
rs13114836	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13139251	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13139533	0.92[EUR][1000 genomes]
rs13145713	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1565217	0.83[EUR][1000 genomes]
rs17472127	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34380340	0.88[EUR][1000 genomes]
rs34386102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34922671	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35079648	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35963236	0.86[EUR][1000 genomes]
rs3811759	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62311260	0.85[EUR][1000 genomes]
rs6447639	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811724	0.81[EUR][1000 genomes]
rs6821909	0.82[EUR][1000 genomes]
rs6824075	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824125	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844692	0.83[EUR][1000 genomes]
rs6847622	0.90[EUR][1000 genomes]
rs745761	0.81[EUR][1000 genomes]
rs7670045	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7676578	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698564	0.90[EUR][1000 genomes];0.81[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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3421012	chr4:48483395-48487593	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6845250	SLC10A4	cis	lung	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48484600-48486600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:48484600-48486600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:48484800-48486200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
4	chr4:48484800-48486600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr4:48484800-48487200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr4:48484800-48487200	Active TSS	A549	lung
7	chr4:48485000-48486200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:48485000-48486200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr4:48485000-48486200	Active TSS	Brain Substantia Nigra	brain
10	chr4:48485000-48486400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:48485000-48486400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:48485000-48486400	Bivalent/Poised TSS	Psoas Muscle	Psoas
13	chr4:48485000-48486400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
14	chr4:48485000-48486600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:48485000-48486600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:48485000-48486600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:48485000-48486600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
18	chr4:48485000-48486600	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr4:48485000-48486800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr4:48485000-48486800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr4:48485000-48486800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
22	chr4:48485000-48488800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:48485200-48486200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr4:48485200-48486200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr4:48485200-48486200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
26	chr4:48485200-48486200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
27	chr4:48485200-48486200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr4:48485200-48486200	Flanking Active TSS	Pancreas	Pancrea
29	chr4:48485200-48486200	Active TSS	K562	blood
30	chr4:48485200-48486400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
31	chr4:48485200-48486800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
32	chr4:48485200-48490200	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr4:48485400-48486200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:48485400-48486200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
35	chr4:48485400-48486200	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
36	chr4:48485400-48486200	Flanking Active TSS	Lung	lung
37	chr4:48485400-48486200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
38	chr4:48485400-48486200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
39	chr4:48485400-48486200	Bivalent Enhancer	HMEC	breast
40	chr4:48485400-48486400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:48485400-48486400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr4:48485600-48486200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:48485600-48486200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:48485600-48486200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
45	chr4:48485600-48486200	Bivalent/Poised TSS	Thymus	Thymus
46	chr4:48485600-48486200	Bivalent Enhancer	GM12878-XiMat	blood
47	chr4:48485600-48486400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
48	chr4:48485600-48486400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
49	chr4:48485600-48486400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
50	chr4:48485600-48486400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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