Variant report

Variant	rs3768437
Chromosome Location	chr1:227347935-227347936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10127638	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1045285	0.93[CHB][hapmap]
rs1045287	0.93[CHB][hapmap]
rs10495256	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10495257	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11582863	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583489	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs12403775	1.00[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12593	0.86[CHB][hapmap]
rs1319103	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs13376552	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1513609	0.87[AMR][1000 genomes]
rs1929855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297418	0.93[CHB][hapmap]
rs2813956	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2953640	0.94[CEU][hapmap]
rs34111989	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768419	0.93[CHB][hapmap]
rs3768420	0.81[CEU][hapmap];0.93[CHB][hapmap]
rs3795445	0.93[CHB][hapmap]
rs3795446	0.93[CHB][hapmap]
rs3795449	0.93[CHB][hapmap]
rs4146588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653822	1.00[CEU][hapmap]
rs6426578	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426584	0.93[CHB][hapmap];0.88[ASN][1000 genomes]
rs6677602	0.86[CHB][hapmap]
rs66796195	0.83[EUR][1000 genomes]
rs72748174	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72748192	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72748195	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72750169	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72750202	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72753628	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72755321	0.82[AMR][1000 genomes]
rs7355000	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531992	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7540155	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs7540391	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7541033	0.93[CHB][hapmap]
rs7553837	0.85[CEU][hapmap];0.93[CHB][hapmap]
rs7553990	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs938257	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	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
4	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
5	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
6	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
7	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
2	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
3	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
5	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:227316600-227352200	Weak transcription	Gastric	stomach
7	chr1:227317000-227374200	Weak transcription	HepG2	liver
8	chr1:227324200-227348400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:227326600-227355200	Weak transcription	Small Intestine	intestine
10	chr1:227327200-227348200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:227327200-227348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:227328000-227354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:227328400-227350000	Weak transcription	Fetal Brain Male	brain
14	chr1:227328600-227351600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:227328800-227354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:227329600-227358400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
18	chr1:227329800-227348400	Weak transcription	Fetal Brain Female	brain
19	chr1:227331600-227355000	Weak transcription	Brain Anterior Caudate	brain
20	chr1:227331600-227358400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:227332800-227350000	Weak transcription	HMEC	breast
22	chr1:227332800-227350200	Weak transcription	Lung	lung
23	chr1:227332800-227354600	Weak transcription	Ovary	ovary
24	chr1:227333000-227349400	Weak transcription	Placenta	Placenta
25	chr1:227333200-227354800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:227333400-227354000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:227333400-227354400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:227333400-227358400	Weak transcription	Osteobl	bone
29	chr1:227333400-227359000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
32	chr1:227334800-227371800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:227339600-227354000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:227343200-227350600	Weak transcription	Stomach Mucosa	stomach
35	chr1:227343200-227352400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:227343200-227400400	Weak transcription	A549	lung
37	chr1:227343600-227358400	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:227344600-227348200	Strong transcription	HSMM	muscle
39	chr1:227345600-227348200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:227345800-227348200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:227346000-227348000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:227346000-227348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:227346000-227348200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:227346000-227348200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:227346200-227348000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:227346200-227348000	Strong transcription	NHEK	skin
47	chr1:227346200-227348200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:227346200-227348200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:227346200-227348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:227346200-227348200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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