Variant report

Variant	rs6441017
Chromosome Location	chr3:155562072-155562073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:155560729-155562109	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155561226..155562916-chr3:155617758..155619577,2	K562	blood:

Variant related genes	Relation type
SLC33A1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11921267	0.86[EUR][1000 genomes]
rs11927551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1516500	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs171448	0.86[EUR][1000 genomes]
rs358702	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs382534	0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs389761	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390677	0.87[EUR][1000 genomes]
rs407258	0.87[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs422497	0.87[EUR][1000 genomes]
rs439765	0.85[EUR][1000 genomes]
rs452874	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503139	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538514	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62286778	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441019	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6787781	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794232	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616853	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636224	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637645	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638685	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649631	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837201	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842017	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6441017	SLC33A1	cis	parietal	SCAN
rs6441017	PLCH1	cis	cerebellum	SCAN
rs6441017	SLC33A1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155524400-155565800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:155524400-155567400	Weak transcription	Lung	lung
3	chr3:155524400-155569400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:155524600-155563400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:155524600-155568000	Weak transcription	HUVEC	blood vessel
6	chr3:155530600-155569800	Weak transcription	Aorta	Aorta
7	chr3:155533400-155565800	Weak transcription	HepG2	liver
8	chr3:155533400-155569400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:155535000-155568000	Weak transcription	Right Ventricle	heart
10	chr3:155535400-155568800	Weak transcription	Osteobl	bone
11	chr3:155535600-155568000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:155536800-155568200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:155537200-155565600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:155537400-155564000	Weak transcription	Fetal Brain Female	brain
15	chr3:155540000-155569400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:155540200-155568000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:155541000-155568000	Weak transcription	Psoas Muscle	Psoas
18	chr3:155541200-155567400	Weak transcription	Ovary	ovary
19	chr3:155541600-155567800	Weak transcription	Colonic Mucosa	Colon
20	chr3:155541800-155565800	Weak transcription	NHDF-Ad	bronchial
21	chr3:155541800-155566000	Weak transcription	Small Intestine	intestine
22	chr3:155542800-155569600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:155543000-155566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:155543000-155569400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:155543000-155569400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:155543000-155569400	Weak transcription	NHLF	lung
27	chr3:155543000-155570200	Weak transcription	Esophagus	oesophagus
28	chr3:155543200-155562400	Weak transcription	Left Ventricle	heart
29	chr3:155543200-155569400	Weak transcription	A549	lung
30	chr3:155544200-155569000	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:155544800-155565800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:155545600-155563000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:155545600-155567200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:155545600-155568000	Weak transcription	Fetal Kidney	kidney
35	chr3:155547400-155563200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:155547600-155565800	Weak transcription	Thymus	Thymus
37	chr3:155547600-155567200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:155547800-155563200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:155547800-155563800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:155547800-155565800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:155547800-155565800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:155547800-155567000	Weak transcription	Hela-S3	cervix
43	chr3:155547800-155567200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:155547800-155568000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:155547800-155569000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:155547800-155569400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:155547800-155569600	Weak transcription	HSMMtube	muscle
48	chr3:155548400-155565400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:155549000-155563000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:155549000-155563200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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