Variant report

Variant	rs6656653
Chromosome Location	chr1:227491874-227491875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227490028..227493033-chr1:227499168..227502183,4	K562	blood:
2	chr1:227489924..227492809-chr1:227503350..227506975,4	K562	blood:
3	chr1:227491263..227493925-chr1:227500068..227502093,2	MCF-7	breast:
4	chr1:227480441..227495625-chr1:227496855..227507828,32	K562	blood:
5	chr1:227490333..227492238-chr1:227505333..227507349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10429872	0.81[EUR][1000 genomes]
rs10495255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737428	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10753433	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799409	0.84[AMR][1000 genomes]
rs10799410	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916108	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10916111	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10916118	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916122	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12065126	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12137591	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12565871	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12566059	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12569227	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2102638	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34084723	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34875093	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35738984	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3795457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339829	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653812	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653823	0.97[ASN][1000 genomes]
rs4653824	0.97[ASN][1000 genomes]
rs4653825	0.96[ASN][1000 genomes]
rs60197034	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682120	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6684784	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6684803	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6685106	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6692294	0.81[AMR][1000 genomes]
rs6697272	0.81[AMR][1000 genomes]
rs6700730	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759337	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516326	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537038	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs955704	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227469200-227500200	Weak transcription	Left Ventricle	heart
3	chr1:227469200-227502600	Weak transcription	HSMM	muscle
4	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
5	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:227475200-227500200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227483600-227500200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:227483800-227500400	Weak transcription	Right Atrium	heart
9	chr1:227486600-227494000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:227486600-227494000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:227486600-227497800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:227487000-227495800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:227487000-227496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:227487000-227496200	Weak transcription	Fetal Heart	heart
15	chr1:227487000-227500200	Weak transcription	HMEC	breast
16	chr1:227487000-227501800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:227487000-227501800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:227487000-227502000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:227487200-227494000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:227487400-227493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:227487400-227494000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:227487600-227496800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:227487600-227497600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:227487600-227502400	Weak transcription	Osteobl	bone
25	chr1:227487800-227492400	Weak transcription	NHDF-Ad	bronchial
26	chr1:227487800-227494200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:227487800-227496000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:227487800-227496000	Weak transcription	Adipose Nuclei	Adipose
29	chr1:227487800-227497000	Weak transcription	Fetal Lung	lung
30	chr1:227487800-227497200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:227487800-227500200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:227487800-227500400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:227487800-227501400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:227488000-227494800	Weak transcription	Brain Anterior Caudate	brain
35	chr1:227488000-227496400	Weak transcription	Hela-S3	cervix
36	chr1:227488000-227501800	Weak transcription	A549	lung
37	chr1:227488400-227496400	Weak transcription	HUVEC	blood vessel
38	chr1:227488800-227493800	Weak transcription	Stomach Mucosa	stomach
39	chr1:227489800-227492000	Enhancers	K562	blood
40	chr1:227490200-227503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:227490400-227492400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:227490600-227496400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:227491000-227494000	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:227491200-227492000	Enhancers	Brain Angular Gyrus	brain
45	chr1:227491200-227492000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:227491400-227501400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:227491600-227499200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:227491800-227492000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:227491800-227492200	Enhancers	Psoas Muscle	Psoas
50	chr1:227491800-227497800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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