Variant report

Variant	rs6807856
Chromosome Location	chr3:23949030-23949031
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	chr3:23946806..23949450-chr3:23951534..23953595,2	MCF-7	breast:
2	chr3:23916758..23918575-chr3:23949004..23951255,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12631785	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4024642	0.93[ASN][1000 genomes]
rs4241514	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241517	0.84[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4321479	0.80[CEU][hapmap];0.92[TSI][hapmap]
rs4589882	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs4858094	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs4858095	0.90[TSI][hapmap]
rs4858551	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858552	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs4858553	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858567	0.80[CEU][hapmap];0.92[TSI][hapmap]
rs4858569	0.84[CEU][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs5023610	0.80[CEU][hapmap]
rs6550815	0.80[EUR][1000 genomes]
rs6550823	0.80[CEU][hapmap];0.92[TSI][hapmap]
rs6550829	0.86[MKK][hapmap]
rs6762238	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6764154	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6779476	0.84[CEU][hapmap];0.90[TSI][hapmap]
rs6794905	0.84[MEX][hapmap]
rs6794922	0.80[CEU][hapmap];0.92[TSI][hapmap]
rs7371944	0.90[TSI][hapmap]
rs7615255	0.91[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs7626431	0.84[CEU][hapmap]
rs7636810	0.88[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7651185	0.91[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap]
rs9830778	0.85[JPT][hapmap]
rs9842907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[EUR][1000 genomes]
rs9845287	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9853532	0.87[EUR][1000 genomes]

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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6807856	C3orf48	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23916000-23950200	Weak transcription	Aorta	Aorta
2	chr3:23922400-23956600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:23923000-23956600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:23923400-23955200	Weak transcription	Thymus	Thymus
5	chr3:23923400-23957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:23923600-23956800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:23924200-23957800	Weak transcription	Esophagus	oesophagus
8	chr3:23924200-23957800	Weak transcription	Lung	lung
9	chr3:23928000-23957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:23928800-23956000	Weak transcription	Small Intestine	intestine
11	chr3:23928800-23957400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:23929000-23956600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:23930800-23954800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:23930800-23956800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:23932000-23955400	Weak transcription	NHEK	skin
16	chr3:23934200-23956600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:23934400-23956400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:23935000-23957400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:23935800-23954400	Weak transcription	NH-A	brain
20	chr3:23935800-23954600	Weak transcription	HUVEC	blood vessel
21	chr3:23936400-23951600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:23936400-23951800	Weak transcription	Spleen	Spleen
23	chr3:23936400-23956400	Weak transcription	Psoas Muscle	Psoas
24	chr3:23936800-23957200	Weak transcription	Brain Substantia Nigra	brain
25	chr3:23937000-23956600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:23939800-23956600	Weak transcription	Fetal Brain Male	brain
27	chr3:23940400-23956600	Weak transcription	Pancreas	Pancrea
28	chr3:23940600-23950800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:23940600-23956600	Weak transcription	Brain Germinal Matrix	brain
30	chr3:23940600-23956800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:23940800-23955400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:23940800-23956200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:23940800-23956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:23940800-23956400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:23940800-23956600	Weak transcription	Left Ventricle	heart
36	chr3:23940800-23956600	Weak transcription	NHLF	lung
37	chr3:23940800-23957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:23940800-23957200	Weak transcription	Right Ventricle	heart
39	chr3:23941000-23951200	Weak transcription	Fetal Lung	lung
40	chr3:23941000-23956000	Weak transcription	HMEC	breast
41	chr3:23941000-23956600	Weak transcription	Primary B cells from cord blood	blood
42	chr3:23941200-23951800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:23941200-23952400	Weak transcription	Fetal Brain Female	brain
44	chr3:23941200-23955200	Weak transcription	Fetal Kidney	kidney
45	chr3:23941200-23956200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:23941200-23956400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:23941400-23950400	Weak transcription	Brain Anterior Caudate	brain
48	chr3:23941400-23956400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:23941400-23956800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:23941800-23951800	Weak transcription	Monocytes-CD14+_RO01746	blood

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