Variant report

Variant	rs73098390
Chromosome Location	chr1:227491060-227491061
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227484375..227486737-chr1:227489822..227491362,2	K562	blood:
2	chr1:227490028..227493033-chr1:227499168..227502183,4	K562	blood:
3	chr1:227489924..227492809-chr1:227503350..227506975,4	K562	blood:
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: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1015815	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1015816	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10916109	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916114	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11801994	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803590	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803761	0.90[EUR][1000 genomes]
rs11805298	0.90[EUR][1000 genomes]
rs11806511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11806937	0.90[EUR][1000 genomes]
rs11808928	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11810328	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11811358	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12402456	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12403650	0.92[EUR][1000 genomes]
rs12403986	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12405363	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12408913	0.92[EUR][1000 genomes]
rs12410327	0.95[EUR][1000 genomes]
rs12741049	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1464076	0.95[EUR][1000 genomes]
rs1464077	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1513602	0.94[EUR][1000 genomes]
rs1513603	0.90[EUR][1000 genomes]
rs1546557	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1606549	0.93[EUR][1000 genomes]
rs16847492	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16847634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17613166	0.92[EUR][1000 genomes]
rs34125608	0.84[AFR][1000 genomes]
rs34263105	0.95[EUR][1000 genomes]
rs34400564	0.90[EUR][1000 genomes]
rs41270149	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4255349	0.94[EUR][1000 genomes]
rs4282782	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4300186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4354510	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4434814	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4437846	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4518864	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4543764	0.88[EUR][1000 genomes]
rs55805110	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55882852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55946024	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57276421	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57758974	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58489467	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59116340	0.90[EUR][1000 genomes]
rs59121440	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59859849	0.94[EUR][1000 genomes]
rs60068245	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60235610	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60742095	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60958272	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61081394	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61522132	0.90[EUR][1000 genomes]
rs6659506	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6668367	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73088658	0.90[EUR][1000 genomes]
rs73090612	0.90[EUR][1000 genomes]
rs73094351	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73094393	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73094400	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096317	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096350	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096353	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096358	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73096374	0.96[EUR][1000 genomes]
rs73098394	0.81[AFR][1000 genomes]
rs73098398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102307	0.95[EUR][1000 genomes]
rs74140153	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7515739	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7519099	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7526283	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7534286	0.87[EUR][1000 genomes]
rs7535010	0.87[EUR][1000 genomes]
rs7539037	0.90[EUR][1000 genomes]
rs7539750	0.90[EUR][1000 genomes]
rs7542505	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7544923	0.93[EUR][1000 genomes]
rs7545775	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7551556	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[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:53 , 50 per page) page: 1 2

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	chr1:227475000-227491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:227475200-227500200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:227478000-227491800	Weak transcription	Psoas Muscle	Psoas
9	chr1:227483600-227500200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:227483800-227500400	Weak transcription	Right Atrium	heart
11	chr1:227485600-227491200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:227486600-227491200	Weak transcription	Aorta	Aorta
13	chr1:227486600-227494000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:227486600-227494000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:227486600-227497800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:227487000-227495800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:227487000-227496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:227487000-227496200	Weak transcription	Fetal Heart	heart
19	chr1:227487000-227500200	Weak transcription	HMEC	breast
20	chr1:227487000-227501800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:227487000-227501800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:227487000-227502000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:227487200-227494000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:227487400-227493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:227487400-227494000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:227487600-227496800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:227487600-227497600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:227487600-227502400	Weak transcription	Osteobl	bone
29	chr1:227487800-227492400	Weak transcription	NHDF-Ad	bronchial
30	chr1:227487800-227494200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:227487800-227496000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:227487800-227496000	Weak transcription	Adipose Nuclei	Adipose
33	chr1:227487800-227497000	Weak transcription	Fetal Lung	lung
34	chr1:227487800-227497200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:227487800-227500200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:227487800-227500400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227487800-227501400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:227488000-227491200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:227488000-227494800	Weak transcription	Brain Anterior Caudate	brain
40	chr1:227488000-227496400	Weak transcription	Hela-S3	cervix
41	chr1:227488000-227501800	Weak transcription	A549	lung
42	chr1:227488400-227496400	Weak transcription	HUVEC	blood vessel
43	chr1:227488800-227493800	Weak transcription	Stomach Mucosa	stomach
44	chr1:227489800-227491600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:227489800-227492000	Enhancers	K562	blood
46	chr1:227490200-227503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:227490400-227491200	Weak transcription	Brain Angular Gyrus	brain
48	chr1:227490400-227492400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:227490600-227496400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:227490800-227491400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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