Variant report

Variant	rs3800324
Chromosome Location	chr6:28264681-28264682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28262644..28265417-chr6:28284862..28286533,2	MCF-7	breast:
2	chr6:28263544..28266110-chr6:28280477..28282083,2	K562	blood:
3	chr6:28264442..28268560-chr6:28269964..28273646,5	K562	blood:
4	chr6:28252167..28254655-chr6:28264060..28265912,2	MCF-7	breast:
5	chr6:28264329..28266427-chr6:28269486..28272144,3	K562	blood:
6	chr6:28255421..28258446-chr6:28262353..28265432,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484542	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233710	0.82[AMR][1000 genomes]
rs1416919	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893917	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893975	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2077474	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs213233	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2159275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281040	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281041	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800327	0.81[AMR][1000 genomes]
rs4711167	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713159	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58019071	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59598126	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60568488	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60698636	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723475	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs723476	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73742535	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73742536	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73742539	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73742541	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73742545	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs742107	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs758397	0.93[EUR][1000 genomes];0.84[ASN][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28265600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:28250600-28267000	Weak transcription	NHEK	skin
8	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
9	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
11	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
13	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:28255200-28268600	Weak transcription	Ovary	ovary
17	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
20	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
21	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
23	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:28255400-28278400	Weak transcription	HepG2	liver
26	chr6:28255600-28264800	Weak transcription	HUVEC	blood vessel
27	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
28	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
29	chr6:28256000-28267600	Weak transcription	Osteobl	bone
30	chr6:28256400-28264800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:28256400-28268400	Weak transcription	Fetal Intestine Large	intestine
32	chr6:28256400-28271600	Weak transcription	Liver	Liver
33	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:28256600-28268200	Weak transcription	Lung	lung
35	chr6:28256600-28268600	Weak transcription	Fetal Thymus	thymus
36	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:28257600-28264800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:28257600-28264800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28257600-28264800	Weak transcription	Dnd41	blood
40	chr6:28257600-28268000	Weak transcription	K562	blood
41	chr6:28257600-28268400	Weak transcription	Right Ventricle	heart
42	chr6:28257600-28278800	Weak transcription	NHDF-Ad	bronchial
43	chr6:28257800-28268600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:28257800-28279000	Weak transcription	HMEC	breast
45	chr6:28258000-28268200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:28258000-28268600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:28258000-28268800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:28258000-28270800	Weak transcription	NH-A	brain
49	chr6:28258200-28268000	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:28258200-28268600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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