Variant report

Variant	rs9444521
Chromosome Location	chr6:88309583-88309584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88300436..88304356-chr6:88305861..88309850,4	MCF-7	breast:
2	chr6:88304887..88306495-chr6:88308043..88310428,2	K562	blood:
3	chr6:88297593..88299984-chr6:88307638..88311850,3	K562	blood:
4	chr6:88307345..88309844-chr6:88410564..88412300,2	MCF-7	breast:
5	chr6:88307562..88310248-chr6:88408505..88411204,2	K562	blood:
6	chr6:88307033..88309962-chr6:88337363..88340137,2	MCF-7	breast:
7	chr6:88306632..88310248-chr6:88408028..88412001,4	K562	blood:

Variant related genes	Relation type
ENSG00000135336	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1075665	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11970493	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12529993	0.86[ASN][1000 genomes]
rs12530371	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34513746	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4132446	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4354121	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707378	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4707385	0.82[EUR][1000 genomes]
rs58305152	0.85[ASN][1000 genomes]
rs6454634	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914244	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294384	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9444513	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9444514	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444516	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444531	0.85[EUR][1000 genomes]
rs9444534	0.81[EUR][1000 genomes]
rs9450728	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450729	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450734	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450735	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450740	0.84[ASN][1000 genomes]
rs9450741	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450743	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450749	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450750	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450751	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450760	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450763	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9444521	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300400-88320800	Weak transcription	Spleen	Spleen
2	chr6:88300400-88323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:88300600-88315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:88300600-88320000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:88300600-88321800	Weak transcription	Lung	lung
6	chr6:88300600-88323400	Weak transcription	Gastric	stomach
7	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
8	chr6:88300800-88311600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:88300800-88320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:88300800-88323600	Weak transcription	Aorta	Aorta
11	chr6:88301000-88310000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:88301000-88311600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:88301000-88313800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:88301000-88315600	Weak transcription	NH-A	brain
15	chr6:88301000-88316400	Weak transcription	Pancreas	Pancrea
16	chr6:88301000-88321000	Weak transcription	Brain Angular Gyrus	brain
17	chr6:88301000-88321000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:88301000-88323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:88301000-88330200	Weak transcription	Right Ventricle	heart
20	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
21	chr6:88301200-88313000	Weak transcription	NHDF-Ad	bronchial
22	chr6:88301200-88313200	Weak transcription	Hela-S3	cervix
23	chr6:88301200-88314000	Weak transcription	HMEC	breast
24	chr6:88301200-88316200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:88301200-88320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:88301200-88320800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:88301200-88323400	Weak transcription	Thymus	Thymus
28	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:88301400-88313000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:88301400-88320800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:88301400-88321000	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:88301400-88322400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:88301400-88338400	Weak transcription	NHLF	lung
34	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:88301600-88320800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:88301800-88319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:88302800-88318800	Weak transcription	HepG2	liver
42	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:88305200-88316200	Weak transcription	K562	blood
44	chr6:88305200-88329000	Weak transcription	HSMMtube	muscle
45	chr6:88305400-88313800	Weak transcription	A549	lung
46	chr6:88305400-88315800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:88305400-88315800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:88305400-88316000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:88305400-88316000	Weak transcription	GM12878-XiMat	blood
50	chr6:88305400-88316200	Weak transcription	H9 Cell Line	embryonic stem cell

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