Variant report

Variant	rs2300900
Chromosome Location	chr6:88188253-88188254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88181342..88183301-chr6:88187144..88189182,2	K562	blood:
2	chr6:88187817..88189806-chr6:88192099..88194936,2	MCF-7	breast:
3	chr6:88181182..88183795-chr6:88188023..88191359,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164414	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10944310	0.90[CHB][hapmap]
rs10944311	0.80[ASN][1000 genomes]
rs11962148	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11965562	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs11970696	0.90[CHB][hapmap]
rs12524203	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12524205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525533	0.80[ASN][1000 genomes]
rs12530371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13195393	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214442	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs16879887	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs16879893	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092647	0.80[ASN][1000 genomes]
rs2092648	0.80[ASN][1000 genomes]
rs2092649	0.84[ASN][1000 genomes]
rs2143890	0.92[ASN][1000 genomes]
rs2223877	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs2246051	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2246057	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2268995	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268996	0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295088	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2300898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300899	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300904	0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2300907	0.91[ASN][1000 genomes]
rs2300908	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2325062	0.80[ASN][1000 genomes]
rs3778671	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4354121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs58785365	0.90[ASN][1000 genomes]
rs6454634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6903332	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909585	0.83[ASN][1000 genomes]
rs6915077	0.90[CHB][hapmap]
rs6927171	0.90[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs6928057	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6931177	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728582	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs7383567	0.88[ASN][1000 genomes]
rs7649	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs7759462	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7761943	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444499	0.90[CHB][hapmap]
rs9444501	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs9444509	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9444511	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444514	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9450659	0.86[CHB][hapmap]
rs9450667	0.90[CHB][hapmap]
rs9450677	0.89[CHB][hapmap]
rs9450681	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs9450686	0.90[CHB][hapmap]
rs9450693	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs9450694	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs9450697	0.89[CHB][hapmap]
rs9450698	0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs9450699	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9450700	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9450702	0.83[ASN][1000 genomes]
rs9450708	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450709	0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450711	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450716	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450717	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450719	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450721	0.87[ASN][1000 genomes]
rs9450740	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs9450749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9450750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs9450751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9450756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2300900	AKIRIN2	cis	cerebellum	SCAN
rs2300900	SLC35A1	cis	parietal	SCAN
rs2300900	SLC35A1	cis	multi-tissue	Pritchard
rs2300900	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2300900	C6orf162	cis	cerebellum	SCAN
rs2300900	C6orf162	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88190200	Weak transcription	Spleen	Spleen
2	chr6:88183600-88193000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:88183600-88193200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:88183600-88193200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:88183600-88193200	Weak transcription	Lung	lung
6	chr6:88183600-88193400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:88183600-88193600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:88183600-88212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:88183600-88226000	Weak transcription	Gastric	stomach
10	chr6:88183800-88188400	Weak transcription	Fetal Stomach	stomach
11	chr6:88183800-88190000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:88183800-88193000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:88183800-88193000	Weak transcription	Esophagus	oesophagus
14	chr6:88183800-88193000	Weak transcription	Fetal Intestine Small	intestine
15	chr6:88183800-88193200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:88183800-88193200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:88183800-88193200	Weak transcription	Placenta	Placenta
18	chr6:88183800-88193600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:88183800-88193800	Weak transcription	Colonic Mucosa	Colon
20	chr6:88183800-88197000	Weak transcription	NH-A	brain
21	chr6:88183800-88204200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:88183800-88210800	Weak transcription	Adipose Nuclei	Adipose
23	chr6:88183800-88211000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:88183800-88211000	Weak transcription	Brain Anterior Caudate	brain
25	chr6:88183800-88211000	Weak transcription	Thymus	Thymus
26	chr6:88183800-88211800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:88183800-88212000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:88183800-88212600	Weak transcription	Psoas Muscle	Psoas
29	chr6:88183800-88216400	Weak transcription	K562	blood
30	chr6:88183800-88219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:88183800-88221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:88183800-88221000	Weak transcription	Fetal Kidney	kidney
33	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
34	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
35	chr6:88184000-88193400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:88184000-88193400	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:88184000-88200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:88184000-88202400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:88184000-88210800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:88184000-88211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:88184000-88211000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:88184000-88218600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:88184000-88218600	Weak transcription	Brain Angular Gyrus	brain
44	chr6:88184000-88218800	Weak transcription	Brain Germinal Matrix	brain
45	chr6:88184000-88219800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:88184000-88221000	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:88184000-88224200	Weak transcription	Hela-S3	cervix
48	chr6:88184200-88193400	Weak transcription	HSMM	muscle
49	chr6:88184200-88211000	Weak transcription	NHDF-Ad	bronchial
50	chr6:88184200-88214800	Weak transcription	Fetal Brain Male	brain

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