Variant report

Variant	rs9444529
Chromosome Location	chr6:88338373-88338374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88323620..88325192-chr6:88338227..88341168,2	K562	blood:
2	chr6:88331042..88333534-chr6:88337714..88340055,2	K562	blood:
3	chr6:88337338..88339717-chr6:88379003..88381353,2	K562	blood:
4	chr6:88307033..88309962-chr6:88337363..88340137,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11965607	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12663400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13213729	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13220363	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35773999	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4330517	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4552702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4707380	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6911782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7748693	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7756133	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768566	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772351	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910267	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444515	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450725	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450727	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450730	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450731	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450756	0.82[CHB][hapmap]
rs9450757	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450759	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450765	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9444529	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444529	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 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	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
3	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:88301400-88338400	Weak transcription	NHLF	lung
5	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
12	chr6:88312200-88371200	Weak transcription	NHEK	skin
13	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
14	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
15	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
17	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
19	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:88321200-88348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:88322000-88346200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:88322600-88344800	Weak transcription	HMEC	breast
25	chr6:88322800-88338400	Weak transcription	Osteobl	bone
26	chr6:88322800-88344000	Weak transcription	Liver	Liver
27	chr6:88322800-88344800	Weak transcription	NH-A	brain
28	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:88323000-88342000	Weak transcription	K562	blood
30	chr6:88323000-88344600	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:88323000-88344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:88323000-88346200	Weak transcription	Fetal Kidney	kidney
33	chr6:88323000-88366400	Weak transcription	A549	lung
34	chr6:88324000-88344000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:88324000-88347400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:88324000-88385000	Weak transcription	Gastric	stomach
38	chr6:88324200-88339200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:88324200-88339800	Weak transcription	Ovary	ovary
40	chr6:88324200-88344800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr6:88324200-88346000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:88324200-88346200	Weak transcription	Fetal Brain Female	brain
43	chr6:88324200-88350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:88324200-88366600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:88324200-88369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:88324200-88370200	Weak transcription	Psoas Muscle	Psoas
47	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr6:88324400-88344600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr6:88324800-88341400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links