Variant report

Variant	rs646754
Chromosome Location	chr1:176146621-176146622
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	chr1:176145023..176147721-chr1:176151866..176154637,2	K562	blood:
2	chr1:176145023..176148582-chr1:176151317..176154637,3	K562	blood:

Variant related genes	Relation type
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10429846	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798430	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798435	1.00[CHB][hapmap]
rs10798443	0.81[AFR][1000 genomes]
rs10913125	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481629	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481632	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481637	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481640	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481648	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2481649	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481650	0.80[AFR][1000 genomes]
rs2481652	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502821	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502827	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502828	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502833	1.00[ASN][1000 genomes]
rs2502837	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774925	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233165	1.00[CHB][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298689	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379645	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460596	1.00[CHB][hapmap]
rs4652146	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508320	0.93[AFR][1000 genomes]
rs533299	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537407	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598855	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613965	1.00[CHB][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821055	1.00[ASN][1000 genomes]
rs6425369	1.00[CHB][hapmap]
rs6425372	1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425373	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425374	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704828	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704833	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7525112	1.00[CHB][hapmap]
rs7532122	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541563	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554913	1.00[CHB][hapmap]
rs791748	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425444	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs998631	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
2	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
3	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
4	chr1:176110600-176164000	Weak transcription	NHLF	lung
5	chr1:176123800-176150000	Weak transcription	Osteobl	bone
6	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
7	chr1:176127000-176147000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:176128000-176147000	Weak transcription	Stomach Mucosa	stomach
13	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
14	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
15	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:176128600-176147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:176128600-176147200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:176128800-176154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:176132200-176154200	Weak transcription	NH-A	brain
23	chr1:176134400-176152800	Weak transcription	Brain Angular Gyrus	brain
24	chr1:176136200-176147400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
26	chr1:176138200-176155800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:176138800-176155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:176139000-176153800	Strong transcription	Dnd41	blood
29	chr1:176139800-176149200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:176139800-176152600	Weak transcription	Brain Anterior Caudate	brain
31	chr1:176140000-176155800	Weak transcription	Fetal Brain Female	brain
32	chr1:176140000-176157800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:176140000-176168200	Weak transcription	Psoas Muscle	Psoas
34	chr1:176140200-176150200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:176140200-176152200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:176140600-176148200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:176140800-176146800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:176140800-176148400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:176140800-176149200	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:176140800-176153600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:176140800-176155800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:176141800-176147400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:176142200-176149200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:176142200-176149200	Weak transcription	Hela-S3	cervix
45	chr1:176142200-176153400	Weak transcription	Fetal Heart	heart
46	chr1:176142200-176154400	Weak transcription	Fetal Kidney	kidney
47	chr1:176142400-176149600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:176142800-176149800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:176142800-176157800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:176142800-176162200	Weak transcription	HepG2	liver

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