Variant report

Variant	rs16889440
Chromosome Location	chr6:24544967-24544968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24539832..24541848-chr6:24544860..24546446,2	MCF-7	breast:
2	chr6:24534085..24537392-chr6:24543907..24547453,3	K562	blood:
3	chr6:24541947..24545276-chr6:24695054..24697889,3	MCF-7	breast:
4	chr6:24544075..24545945-chr6:24559657..24561591,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2076313	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs2243831	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs2267539	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2744542	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs2744543	0.92[CHB][hapmap]
rs2744544	0.92[CHB][hapmap]
rs2760165	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs2760166	0.92[CHB][hapmap]
rs2760172	0.92[CHB][hapmap]
rs2760173	0.92[CHB][hapmap]
rs2760174	0.92[CHB][hapmap]
rs2760175	0.92[CHB][hapmap]
rs2760179	0.84[CHB][hapmap]
rs2817237	0.86[ASN][1000 genomes]
rs2817245	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs2817250	0.92[CHB][hapmap]
rs2817251	0.92[CHB][hapmap]
rs2817253	0.92[CHB][hapmap]
rs2817254	0.92[CHB][hapmap]
rs2817255	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs55957932	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456617	0.82[CHB][hapmap]
rs6911965	0.84[CHB][hapmap]
rs6921564	0.84[ASN][1000 genomes]
rs72834964	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7767225	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467220	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs9467231	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Radiation response	20923822	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16889440	BTN1A1	cis	cerebellum	SCAN
rs16889440	GMNN	cis	parietal	SCAN
rs16889440	HIST1H3B	cis	parietal	SCAN
rs16889440	HIST1H2BA	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
2	chr6:24509400-24545800	Weak transcription	Small Intestine	intestine
3	chr6:24532200-24545000	Weak transcription	K562	blood
4	chr6:24535000-24546200	Weak transcription	Pancreas	Pancrea
5	chr6:24535000-24547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:24535200-24566600	Weak transcription	Brain Germinal Matrix	brain
7	chr6:24535200-24591200	Weak transcription	Fetal Brain Male	brain
8	chr6:24535400-24550000	Weak transcription	Gastric	stomach
9	chr6:24535600-24546000	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:24535600-24546800	Weak transcription	Dnd41	blood
11	chr6:24535600-24547400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:24535600-24560600	Weak transcription	Brain Anterior Caudate	brain
13	chr6:24535600-24560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:24535600-24563200	Weak transcription	Brain Angular Gyrus	brain
15	chr6:24535600-24583400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:24537000-24545400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:24537000-24546200	Weak transcription	Fetal Heart	heart
18	chr6:24538200-24545800	Weak transcription	Aorta	Aorta
19	chr6:24538200-24546000	Weak transcription	HepG2	liver
20	chr6:24538200-24547400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:24538400-24547400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:24539200-24583200	Weak transcription	Fetal Intestine Small	intestine
23	chr6:24540200-24556200	Weak transcription	Fetal Brain Female	brain
24	chr6:24540800-24546400	Weak transcription	Liver	Liver
25	chr6:24540800-24547400	Weak transcription	Fetal Thymus	thymus
26	chr6:24540800-24547400	Weak transcription	Thymus	Thymus
27	chr6:24540800-24547600	Weak transcription	Fetal Stomach	stomach
28	chr6:24544800-24546200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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