Variant report

Variant	rs28370666
Chromosome Location	chr12:40414116-40414117
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40413403..40416172-chr12:40500145..40501731,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10454013	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10506141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877929	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878029	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11174735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174918	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11174998	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175021	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175027	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175090	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175094	0.85[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175106	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175409	0.87[ASN][1000 genomes]
rs11175456	0.87[ASN][1000 genomes]
rs11564157	0.87[ASN][1000 genomes]
rs11564215	0.83[EUR][1000 genomes]
rs11564279	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12228213	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1542594	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17518099	1.00[YRI][hapmap]
rs1871895	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2101144	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2128276	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2200085	0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242367	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2708445	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28370636	0.95[EUR][1000 genomes]
rs28370645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28370647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4533099	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61931530	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61933163	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7135815	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301226	0.87[ASN][1000 genomes]
rs7302006	0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7953143	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7966132	0.81[ASN][1000 genomes]
rs7966741	0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7967369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967822	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7973688	0.87[ASN][1000 genomes]
rs7975693	0.85[JPT][hapmap];1.00[YRI][hapmap]

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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:40405400-40445200	Weak transcription	K562	blood
4	chr12:40405600-40417000	Weak transcription	Lung	lung
5	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
6	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
8	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:40406600-40425800	Weak transcription	Liver	Liver
11	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:40410000-40417200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:40410000-40422200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:40411000-40417000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:40411000-40418800	Weak transcription	Aorta	Aorta
17	chr12:40411400-40416800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:40411600-40416800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:40411600-40418800	Weak transcription	Right Atrium	heart
22	chr12:40411600-40422000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:40411600-40424000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:40411600-40425600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
26	chr12:40411800-40425200	Weak transcription	Fetal Intestine Small	intestine
27	chr12:40411800-40425600	Weak transcription	Fetal Intestine Large	intestine
28	chr12:40411800-40425600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
30	chr12:40412400-40417200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr12:40412400-40417400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:40412600-40417000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr12:40412800-40414400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr12:40412800-40415800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr12:40412800-40417200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:40413000-40414200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:40413000-40415200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr12:40413000-40416000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr12:40413600-40417000	Weak transcription	Brain Germinal Matrix	brain
40	chr12:40413800-40414200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr12:40414000-40414400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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