Variant report

Variant	rs9444514
Chromosome Location	chr6:88254243-88254244
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	chr6:88253112..88256865-chr6:88258252..88260308,4	K562	blood:
2	chr6:88206916..88208573-chr6:88253644..88256312,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1052623	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs10944310	0.85[CHB][hapmap]
rs11962148	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11965562	0.84[CHB][hapmap]
rs11970493	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11970696	0.85[CHB][hapmap]
rs12524205	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs12529993	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12530371	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13214442	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs16879893	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2223877	0.84[CHB][hapmap]
rs2246051	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2246057	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2268996	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2295088	0.88[CHB][hapmap]
rs2300898	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2300899	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2300900	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2300904	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2300908	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs34513746	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778671	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs3818057	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4132446	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4354121	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707378	0.80[EUR][1000 genomes]
rs4707385	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs58305152	0.83[ASN][1000 genomes]
rs6454634	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914244	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6915077	0.85[CHB][hapmap]
rs6927171	0.89[CHB][hapmap]
rs6928057	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs728582	0.84[CHB][hapmap]
rs7649	0.94[CHB][hapmap]
rs7759462	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761943	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs9294385	1.00[JPT][hapmap]
rs9444499	0.85[CHB][hapmap]
rs9444501	0.85[CHB][hapmap]
rs9444509	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs9444511	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444513	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444516	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444521	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450667	0.84[CHB][hapmap]
rs9450677	0.83[CHB][hapmap]
rs9450681	0.84[CHB][hapmap]
rs9450686	0.84[CHB][hapmap]
rs9450693	0.85[CHB][hapmap]
rs9450697	0.83[CHB][hapmap]
rs9450698	0.84[CHB][hapmap]
rs9450699	0.94[CHB][hapmap]
rs9450700	0.94[CHB][hapmap]
rs9450708	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs9450709	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs9450716	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs9450717	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs9450719	0.85[AMR][1000 genomes]
rs9450728	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450729	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450734	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450735	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450740	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9450741	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450743	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450750	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450751	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450756	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450760	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450763	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9474	0.93[CEU][hapmap];1.00[JPT][hapmap]

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	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	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
3	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
4	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
5	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
rs9444514	SLC35A1	cis	multi-tissue	Pritchard
rs9444514	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	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
2	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
3	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
5	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
7	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:88229400-88261600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:88229400-88271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:88229600-88289000	Weak transcription	Lung	lung
11	chr6:88230000-88267000	Weak transcription	Brain Substantia Nigra	brain
12	chr6:88230400-88271200	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:88230600-88254400	Weak transcription	Psoas Muscle	Psoas
14	chr6:88230800-88261600	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:88231200-88262800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:88231200-88264200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:88240600-88268200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:88244800-88254400	Weak transcription	Aorta	Aorta
19	chr6:88248000-88255200	Strong transcription	Osteobl	bone
20	chr6:88248800-88255200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:88248800-88257400	Strong transcription	Placenta	Placenta
22	chr6:88249000-88255000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:88249000-88255000	Strong transcription	HSMM	muscle
24	chr6:88249000-88259600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:88249000-88265600	Strong transcription	HepG2	liver
26	chr6:88249400-88263600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:88249600-88255200	Strong transcription	Liver	Liver
28	chr6:88249600-88259000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:88249800-88254400	Weak transcription	Fetal Kidney	kidney
30	chr6:88250000-88275200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:88250400-88256800	Strong transcription	Primary T cells from cord blood	blood
32	chr6:88250400-88262600	Weak transcription	HMEC	breast
33	chr6:88250600-88256000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr6:88250600-88259000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:88250600-88260000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:88250600-88270800	Weak transcription	Fetal Heart	heart
37	chr6:88250600-88276800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:88250600-88281600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:88250800-88260200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:88250800-88270400	Weak transcription	Pancreas	Pancrea
41	chr6:88251000-88260200	Strong transcription	Fetal Thymus	thymus
42	chr6:88251000-88281800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:88251000-88291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:88251200-88254600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:88251200-88255200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:88251200-88255800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:88251200-88258000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:88251200-88262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:88251200-88263400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:88251200-88270800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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