Variant report

Variant	rs9444531
Chromosome Location	chr6:88378359-88378360
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88377817..88379372-chr6:88381342..88384204,2	K562	blood:
2	chr6:88373813..88376185-chr6:88376280..88379564,3	K562	blood:
3	chr6:88368493..88371498-chr6:88375456..88378461,3	K562	blood:
4	chr6:88377297..88379434-chr6:88381335..88385575,5	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1052623	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1075665	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11962148	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12524205	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12530371	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13214442	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs16879893	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2246051	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2246057	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2268996	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2300898	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2300899	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2300900	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2300904	0.94[JPT][hapmap]
rs2300908	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3778671	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3818057	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4354121	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4707385	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707386	0.90[ASN][1000 genomes]
rs58305152	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6454634	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6914244	0.86[EUR][1000 genomes]
rs6927171	0.81[JPT][hapmap]
rs6928057	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7761943	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9294384	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294385	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9444509	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs9444514	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9444521	0.85[EUR][1000 genomes]
rs9444534	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444536	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450708	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9450709	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9450716	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs9450717	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs9450740	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9450749	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450750	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9450751	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9450756	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9450760	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450763	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450773	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450775	0.83[EUR][1000 genomes]
rs9474	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[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	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
2	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
3	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
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9444531	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444531	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
5	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
6	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
8	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
10	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:88324000-88385000	Weak transcription	Gastric	stomach
13	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:88329800-88383200	Weak transcription	Lung	lung
15	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
17	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:88349200-88381400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:88349400-88385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:88349400-88397400	Weak transcription	Ovary	ovary
22	chr6:88355200-88379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:88356600-88380400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:88358200-88392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:88359800-88381000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:88361000-88380400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
29	chr6:88364400-88384800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:88365000-88390000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:88365400-88379800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:88366400-88390000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:88366600-88390000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:88367600-88380400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:88367800-88380200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:88367800-88380200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:88367800-88380200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:88367800-88385000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:88368000-88380200	Weak transcription	Fetal Intestine Large	intestine
40	chr6:88368000-88382000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr6:88368000-88393400	Weak transcription	Small Intestine	intestine
42	chr6:88368600-88379200	Weak transcription	Thymus	Thymus
43	chr6:88370200-88378800	Weak transcription	Left Ventricle	heart
44	chr6:88370200-88391800	Weak transcription	Fetal Brain Male	brain
45	chr6:88370400-88379200	Weak transcription	HMEC	breast
46	chr6:88370400-88381200	Weak transcription	Aorta	Aorta
47	chr6:88370400-88381400	Weak transcription	HUVEC	blood vessel
48	chr6:88370400-88384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:88371000-88381800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:88371000-88383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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