Variant report

Variant	rs12744825
Chromosome Location	chr1:227286652-227286653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227285309..227287428-chr1:227288705..227291944,3	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1045247	0.87[AFR][1000 genomes]
rs10495259	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10495272	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916079	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11583247	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583340	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11586575	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586734	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12117207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12119153	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs12119448	0.82[EUR][1000 genomes]
rs12121729	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12127665	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12128667	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133428	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12134379	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12136857	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12141838	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12739480	0.89[CEU][hapmap]
rs12747807	0.82[EUR][1000 genomes]
rs12751015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752546	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755437	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12755770	0.85[CEU][hapmap]
rs1320495	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17544956	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17545704	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17546688	0.83[EUR][1000 genomes]
rs17592190	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17601316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17601919	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17602169	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2150874	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34169114	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34556998	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35156994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35651721	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35672262	0.82[EUR][1000 genomes]
rs35817866	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768422	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3768431	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3820651	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4308948	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs61836468	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61836474	0.83[EUR][1000 genomes]
rs6664330	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674640	1.00[YRI][hapmap]
rs6681959	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6695431	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698156	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512871	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs7523759	0.89[CEU][hapmap]
rs7526822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7533684	1.00[YRI][hapmap]
rs7538237	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7543419	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
4	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:227240000-227286800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:227247400-227299800	Weak transcription	HMEC	breast
8	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:227257600-227288000	Weak transcription	HSMMtube	muscle
10	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
12	chr1:227260400-227287800	Weak transcription	NHEK	skin
13	chr1:227261400-227287800	Weak transcription	Osteobl	bone
14	chr1:227268800-227287000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:227271800-227286800	Weak transcription	NHDF-Ad	bronchial
16	chr1:227271800-227287800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:227271800-227288000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:227271800-227299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:227272600-227294400	Weak transcription	Fetal Heart	heart
20	chr1:227272800-227295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:227272800-227295000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:227272800-227331000	Weak transcription	Lung	lung
23	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:227275400-227287000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:227277000-227288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
28	chr1:227279200-227287000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:227279200-227287800	Weak transcription	Aorta	Aorta
30	chr1:227279200-227287800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:227279200-227287800	Weak transcription	Fetal Stomach	stomach
32	chr1:227279400-227286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:227279400-227288000	Weak transcription	NH-A	brain
34	chr1:227279800-227287200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:227279800-227299000	Weak transcription	Placenta	Placenta
36	chr1:227280800-227298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227281800-227294400	Weak transcription	Fetal Kidney	kidney
38	chr1:227282400-227287800	Weak transcription	NHLF	lung
39	chr1:227282400-227288000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:227282600-227287600	Weak transcription	Liver	Liver
41	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:227283000-227287800	Weak transcription	HepG2	liver
43	chr1:227283800-227288600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:227284000-227288800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227284400-227288600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:227284800-227287200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:227284800-227288600	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:227285000-227288600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:227285200-227287200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:227285200-227287400	Strong transcription	Psoas Muscle	Psoas

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