Variant report

Variant	rs1344421
Chromosome Location	chr1:61831057-61831058
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11207728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125778	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12066006	0.93[ASN][1000 genomes]
rs12134760	0.93[ASN][1000 genomes]
rs12741051	0.93[ASN][1000 genomes]
rs12758060	0.90[ASN][1000 genomes]
rs1344420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474873	0.96[ASN][1000 genomes]
rs2103882	0.84[ASN][1000 genomes]
rs2180198	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180199	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207788	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs2886080	0.93[ASN][1000 genomes]
rs41423747	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4406666	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4915735	0.86[ASN][1000 genomes]
rs4915737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4915738	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6587918	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587919	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587920	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587921	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662226	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6662305	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669158	0.84[AMR][1000 genomes]
rs6673795	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674884	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6697762	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697777	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697955	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7512491	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526670	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7553582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436635	0.93[ASN][1000 genomes]
rs9436637	0.88[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
2	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
3	chr1:61805800-61848800	Weak transcription	Pancreas	Pancrea
4	chr1:61810600-61831600	Weak transcription	Stomach Mucosa	stomach
5	chr1:61814000-61848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:61814600-61841200	Weak transcription	Psoas Muscle	Psoas
7	chr1:61814600-61848800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:61818600-61837600	Weak transcription	Fetal Brain Male	brain
9	chr1:61818800-61835800	Weak transcription	Esophagus	oesophagus
10	chr1:61819000-61832800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:61819000-61848800	Weak transcription	Lung	lung
12	chr1:61819200-61832800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:61820600-61834600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:61820600-61836400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:61820600-61840600	Weak transcription	NHEK	skin
16	chr1:61820600-61848800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:61822800-61831600	Strong transcription	Liver	Liver
18	chr1:61823400-61854800	Weak transcription	Spleen	Spleen
19	chr1:61824800-61834000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:61825000-61841200	Weak transcription	Right Ventricle	heart
21	chr1:61825000-61843000	Weak transcription	K562	blood
22	chr1:61825200-61840600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:61825200-61847200	Weak transcription	A549	lung
24	chr1:61825200-61848600	Weak transcription	Hela-S3	cervix
25	chr1:61825200-61849000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:61825200-61849000	Weak transcription	Ovary	ovary
27	chr1:61825400-61837400	Weak transcription	HUVEC	blood vessel
28	chr1:61825400-61840800	Weak transcription	Aorta	Aorta
29	chr1:61825600-61848800	Weak transcription	Gastric	stomach
30	chr1:61826200-61851600	Weak transcription	Fetal Intestine Small	intestine
31	chr1:61826400-61834600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:61826400-61835800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:61826400-61848800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:61827000-61835800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:61827000-61841200	Weak transcription	Left Ventricle	heart
36	chr1:61827000-61848600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:61827000-61849000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:61827200-61835600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:61828200-61832600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:61828200-61833800	Weak transcription	Brain Anterior Caudate	brain
41	chr1:61828200-61836000	Weak transcription	Fetal Lung	lung
42	chr1:61828200-61838200	Weak transcription	Fetal Brain Female	brain
43	chr1:61828200-61848800	Weak transcription	Fetal Intestine Large	intestine
44	chr1:61828200-61854600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:61828400-61831200	Weak transcription	Adipose Nuclei	Adipose
46	chr1:61828400-61832800	Weak transcription	Brain Substantia Nigra	brain
47	chr1:61828400-61834000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:61828400-61839800	Weak transcription	Fetal Stomach	stomach
49	chr1:61828600-61841200	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:61828600-61848800	Weak transcription	Stomach Smooth Muscle	stomach

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