Variant report

Variant	rs60197034
Chromosome Location	chr1:227504078-227504079
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227452777..227456360-chr1:227502343..227504370,3	K562	blood:
2	chr1:227500962..227504758-chr1:227504964..227507747,3	MCF-7	breast:
3	chr1:227486302..227488328-chr1:227502025..227504666,2	K562	blood:
4	chr1:45987049..45987881-chr1:227503644..227504512,2	Hela-S3	cervix:
5	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:

Variant related genes	Relation type
ENSG00000236636	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000242757	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10429872	0.81[EUR][1000 genomes]
rs10495255	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737428	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10753433	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799409	0.82[AMR][1000 genomes]
rs10799410	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916108	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10916111	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10916118	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916122	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12065126	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12137591	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12565871	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12566059	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12569227	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2102638	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34084723	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34875093	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35738984	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3795457	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339829	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653812	0.86[AFR][1000 genomes];0.83[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]
rs6656653	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682120	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6684784	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6684803	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6685106	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6700730	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759337	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516326	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537038	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs955704	0.81[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:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227496200-227504800	Weak transcription	Gastric	stomach
2	chr1:227500600-227504800	Weak transcription	Lung	lung
3	chr1:227500800-227504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:227500800-227504600	Weak transcription	Pancreas	Pancrea
5	chr1:227500800-227506600	Active TSS	K562	blood
6	chr1:227501400-227506800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:227501400-227507000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:227501600-227507000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:227501800-227505400	Active TSS	Right Atrium	heart
10	chr1:227501800-227505600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:227501800-227505800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:227501800-227506600	Active TSS	Fetal Stomach	stomach
13	chr1:227501800-227506600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:227501800-227506600	Active TSS	HMEC	breast
15	chr1:227501800-227506600	Active TSS	NHEK	skin
16	chr1:227501800-227506800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:227501800-227506800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:227501800-227506800	Active TSS	Brain Anterior Caudate	brain
19	chr1:227501800-227506800	Active TSS	A549	lung
20	chr1:227501800-227506800	Active TSS	NHLF	lung
21	chr1:227501800-227507000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:227501800-227507000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:227501800-227507000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:227501800-227507000	Active TSS	Fetal Kidney	kidney
25	chr1:227501800-227507200	Active TSS	Duodenum Mucosa	Duodenum
26	chr1:227501800-227507200	Active TSS	NHDF-Ad	bronchial
27	chr1:227502000-227504600	Active TSS	HepG2	liver
28	chr1:227502000-227506600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:227502000-227506600	Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:227502000-227506600	Active TSS	Colonic Mucosa	Colon
31	chr1:227502000-227506600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr1:227502000-227506600	Active TSS	HUVEC	blood vessel
33	chr1:227502000-227506800	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:227502000-227506800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:227502000-227506800	Active TSS	Stomach Smooth Muscle	stomach
36	chr1:227502000-227506800	Active TSS	NH-A	brain
37	chr1:227502000-227507000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:227502000-227507000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr1:227502000-227507000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:227502000-227507000	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr1:227502000-227507000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:227502000-227507000	Active TSS	Brain Angular Gyrus	brain
43	chr1:227502000-227507000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:227502000-227507000	Active TSS	Brain Substantia Nigra	brain
45	chr1:227502000-227507000	Active TSS	HSMMtube	muscle
46	chr1:227502000-227507200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:227502000-227507200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:227502000-227507200	Active TSS	Psoas Muscle	Psoas
49	chr1:227502200-227505600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:227502200-227506800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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