Variant report

Variant	rs2670470
Chromosome Location	chr1:227452844-227452845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10127638	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10495256	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs12118840	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1513609	0.83[EUR][1000 genomes]
rs1513617	1.00[ASN][1000 genomes]
rs1849550	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1929855	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs2718191	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718214	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718220	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718223	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2813955	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2813956	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2813957	0.90[EUR][1000 genomes]
rs2813977	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2953640	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4146588	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4375224	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653822	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426584	1.00[JPT][hapmap]
rs6426596	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66796195	0.81[ASN][1000 genomes]
rs72753628	0.80[EUR][1000 genomes]
rs72755321	0.89[EUR][1000 genomes]
rs7531992	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7540155	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7540391	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540618	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs938257	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs9700661	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv947163	chr1:227448485-227455052	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2476939	chr1:227451633-227453112	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
5	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
6	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
9	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
11	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
12	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
13	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
17	chr1:227440000-227456600	Weak transcription	HepG2	liver
18	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
19	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:227445800-227458400	Weak transcription	NHEK	skin
21	chr1:227447000-227456800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:227447400-227455000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:227448400-227453600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:227448400-227456400	Weak transcription	Psoas Muscle	Psoas
26	chr1:227448600-227457200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:227449600-227473600	Weak transcription	NH-A	brain
28	chr1:227449800-227453600	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:227449800-227465200	Weak transcription	K562	blood
30	chr1:227452400-227456000	Enhancers	Brain Hippocampus Middle	brain
31	chr1:227452600-227453200	Enhancers	Brain Substantia Nigra	brain
32	chr1:227452800-227453000	Enhancers	Brain Angular Gyrus	brain
33	chr1:227452800-227453000	Enhancers	Brain Anterior Caudate	brain
34	chr1:227452800-227453000	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:227452800-227453000	Enhancers	Lung	lung
36	chr1:227452800-227453400	Enhancers	Ovary	ovary
37	chr1:227452800-227453800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:227452800-227454400	Weak transcription	Stomach Mucosa	stomach
39	chr1:227452800-227463800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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