Variant report

Variant	rs9450721
Chromosome Location	chr6:88219904-88219905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88116466..88118360-chr6:88218142..88220777,2	MCF-7	breast:
2	chr6:88217873..88220227-chr6:88221102..88223244,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213204	Chromatin interaction
ENSG00000272514	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11962148	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12524203	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12524205	0.87[ASN][1000 genomes]
rs13195393	0.87[ASN][1000 genomes]
rs16879893	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2092649	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143890	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246057	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268995	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2268996	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300898	0.87[ASN][1000 genomes]
rs2300899	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300900	0.87[ASN][1000 genomes]
rs2300904	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300908	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778671	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818057	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58785365	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903332	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6927171	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6928057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6931177	0.87[ASN][1000 genomes]
rs7383567	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759462	0.84[ASN][1000 genomes]
rs7761943	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444509	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444511	0.84[ASN][1000 genomes]
rs9450708	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450709	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450711	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450716	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450717	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450719	0.83[EUR][1000 genomes];0.94[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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9450721	SLC35A1	cis	multi-tissue	Pritchard
rs9450721	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88226000	Weak transcription	Gastric	stomach
2	chr6:88183800-88221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:88183800-88221000	Weak transcription	Fetal Kidney	kidney
4	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
5	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
6	chr6:88184000-88221000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:88184000-88224200	Weak transcription	Hela-S3	cervix
8	chr6:88188600-88221600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:88191200-88227400	Weak transcription	Spleen	Spleen
10	chr6:88193600-88227600	Weak transcription	Pancreas	Pancrea
11	chr6:88193800-88220400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:88193800-88221000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:88193800-88221400	Weak transcription	Ovary	ovary
14	chr6:88193800-88227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:88194000-88226200	Weak transcription	Lung	lung
16	chr6:88194000-88249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:88194200-88221400	Weak transcription	Colonic Mucosa	Colon
18	chr6:88194600-88228200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:88198800-88223600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:88200600-88227400	Weak transcription	Small Intestine	intestine
21	chr6:88205200-88224600	Weak transcription	Stomach Mucosa	stomach
22	chr6:88207200-88242600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:88210000-88223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:88210200-88223600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:88210200-88224400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:88210200-88231400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:88210200-88232800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:88210200-88240600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr6:88210400-88235000	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr6:88210800-88224600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:88210800-88224600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:88210800-88230800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:88210800-88230800	Strong transcription	Fetal Thymus	thymus
34	chr6:88210800-88231400	Strong transcription	Osteobl	bone
35	chr6:88210800-88235000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:88211000-88223000	Strong transcription	Primary B cells from cord blood	blood
37	chr6:88211000-88231400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:88211000-88235000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:88211000-88235200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:88211000-88241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:88211200-88220200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr6:88211200-88230800	Strong transcription	Liver	Liver
43	chr6:88211800-88224600	Strong transcription	HUVEC	blood vessel
44	chr6:88212000-88245200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:88212600-88220400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:88212600-88221600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:88212800-88224000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:88212800-88227400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:88213000-88220200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:88213000-88221000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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