Variant report

Variant	rs2953650
Chromosome Location	chr1:227540456-227540457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227539859..227541610-chr1:227547755..227549501,2	K562	blood:
2	chr1:227536339..227538275-chr1:227540360..227541874,2	K562	blood:
3	chr1:227538699..227541484-chr1:227541523..227544732,3	K562	blood:
4	chr1:227538792..227542003-chr1:227542964..227545271,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10495255	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs10753433	0.80[AFR][1000 genomes]
rs12035986	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs12044287	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs12137591	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs12565871	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs2953637	0.86[ASN][1000 genomes]
rs2953638	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2953641	0.95[ASN][1000 genomes]
rs2953643	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953645	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953653	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2953655	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2953656	0.97[ASN][1000 genomes]
rs3014252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs3014253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3014256	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3014263	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3014267	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs3014271	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795457	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs4339829	0.82[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap]
rs955704	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227538400-227541200	Enhancers	HUVEC	blood vessel
2	chr1:227538600-227540600	Enhancers	Left Ventricle	heart
3	chr1:227538600-227540800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:227538600-227540800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:227538800-227540600	Enhancers	Adipose Nuclei	Adipose
6	chr1:227539200-227545000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:227539400-227541800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:227539400-227544400	Weak transcription	Right Atrium	heart
9	chr1:227539400-227544400	Weak transcription	Right Ventricle	heart
10	chr1:227539400-227545000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:227539600-227544200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:227539600-227544200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:227539600-227544200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:227539600-227544200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:227539600-227544200	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:227539600-227544200	Weak transcription	HMEC	breast
17	chr1:227539600-227544200	Weak transcription	HSMM	muscle
18	chr1:227539600-227544200	Weak transcription	NH-A	brain
19	chr1:227539600-227544200	Weak transcription	NHEK	skin
20	chr1:227539600-227544200	Weak transcription	Osteobl	bone
21	chr1:227539600-227544600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:227539600-227544800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:227539800-227543600	Weak transcription	Hela-S3	cervix
24	chr1:227539800-227543800	Weak transcription	A549	lung
25	chr1:227539800-227544200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:227539800-227544200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:227539800-227544400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:227539800-227544400	Weak transcription	HSMMtube	muscle
29	chr1:227540000-227540600	Enhancers	Lung	lung
30	chr1:227540200-227540800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:227540400-227540600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:227540400-227540800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:227540400-227540800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:227540400-227544400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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