Variant report

Variant	rs12130732
Chromosome Location	chr1:227079700-227079701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227072686..227075297-chr1:227079508..227082129,3	K562	blood:
2	chr1:227076139..227079788-chr1:227081535..227086284,4	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799367	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916057	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916059	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11580744	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11588886	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119853	0.88[EUR][1000 genomes]
rs12123818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125811	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12127440	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12138310	0.83[EUR][1000 genomes]
rs12143886	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12403248	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12405779	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12733650	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12747261	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760155	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846644	0.97[EUR][1000 genomes]
rs1800672	0.98[EUR][1000 genomes]
rs1800673	0.98[EUR][1000 genomes]
rs1800681	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236912	0.95[EUR][1000 genomes]
rs3213436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34081886	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35029375	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35213802	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244407	0.82[EUR][1000 genomes]
rs35396772	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35519961	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35744376	0.86[EUR][1000 genomes]
rs3820649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829979	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426554	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680780	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71648404	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732479	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7512804	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
3	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:227069400-227087800	Weak transcription	HMEC	breast
6	chr1:227069400-227102800	Weak transcription	K562	blood
7	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
9	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
10	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
11	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
12	chr1:227071200-227091400	Weak transcription	Osteobl	bone
13	chr1:227071400-227080000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:227071400-227084400	Strong transcription	Fetal Intestine Small	intestine
15	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
17	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
19	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
20	chr1:227072800-227083600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:227073000-227080400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:227073400-227084400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:227073400-227084600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
26	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
27	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:227074200-227080400	Strong transcription	Brain Anterior Caudate	brain
29	chr1:227074200-227081800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:227074200-227083000	Strong transcription	Colon Smooth Muscle	Colon
31	chr1:227074200-227091800	Weak transcription	Fetal Heart	heart
32	chr1:227074600-227079800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:227074800-227090000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:227074800-227090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:227075000-227084200	Strong transcription	Gastric	stomach
36	chr1:227075000-227085400	Strong transcription	Ovary	ovary
37	chr1:227075000-227087400	Weak transcription	Primary B cells from cord blood	blood
38	chr1:227075000-227088800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:227075200-227079800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:227075200-227081200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:227075200-227083200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr1:227075200-227087000	Weak transcription	GM12878-XiMat	blood
43	chr1:227075200-227091800	Weak transcription	Right Atrium	heart
44	chr1:227075400-227080400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:227075400-227081600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:227075400-227085000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:227075400-227088800	Strong transcription	Liver	Liver
48	chr1:227075600-227079800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:227075600-227080600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:227075600-227083200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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