Variant report

Variant	rs6672649
Chromosome Location	chr1:192993353-192993354
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	chr1:192992147..192995725-chr1:192998536..193000592,4	K562	blood:

Variant related genes	Relation type
ENSG00000116750	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10733078	0.88[ASN][1000 genomes]
rs10737620	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10801167	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10801173	0.92[ASN][1000 genomes]
rs10801174	0.90[ASN][1000 genomes]
rs10801175	0.87[ASN][1000 genomes]
rs10921304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10921305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10921308	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10921310	0.90[ASN][1000 genomes]
rs10921312	0.90[ASN][1000 genomes]
rs10921313	0.90[ASN][1000 genomes]
rs11583763	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12086884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12141392	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12735445	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1555555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1890660	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2181408	0.90[ASN][1000 genomes]
rs2275444	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2370079	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2370081	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753948	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806351	0.81[ASN][1000 genomes]
rs3818865	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820417	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3945872	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4657840	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4657842	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657843	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4657845	0.90[ASN][1000 genomes]
rs4657846	0.81[ASN][1000 genomes]
rs4657847	0.81[ASN][1000 genomes]
rs4658079	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663431	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6665069	0.89[ASN][1000 genomes]
rs6671237	0.88[ASN][1000 genomes]
rs6676322	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676416	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6692342	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692805	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6703727	0.89[ASN][1000 genomes]
rs7534257	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7542466	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547615	0.90[ASN][1000 genomes]
rs7553247	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs912070	0.90[ASN][1000 genomes]
rs912071	0.88[ASN][1000 genomes]
rs9427838	0.92[ASN][1000 genomes]
rs9783104	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998429	chr1:192961698-193050515	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv498699	chr1:192970436-192993624	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv3966	chr1:192976457-193004886	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192963800-192994400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:192963800-192996200	Weak transcription	Fetal Lung	lung
3	chr1:192963800-193012400	Weak transcription	NHEK	skin
4	chr1:192963800-193019600	Weak transcription	Ovary	ovary
5	chr1:192964000-192994400	Weak transcription	Left Ventricle	heart
6	chr1:192966200-192994200	Weak transcription	Primary T cells from cord blood	blood
7	chr1:192968000-193009400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:192968000-193012400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:192968000-193019400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:192977600-193005200	Weak transcription	A549	lung
11	chr1:192979000-192994400	Weak transcription	HepG2	liver
12	chr1:192979200-193025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:192981200-192994600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:192981400-192994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:192981400-193026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:192982400-192996400	Weak transcription	Fetal Intestine Small	intestine
17	chr1:192982600-192995800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:192982600-193002400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:192983000-193017800	Weak transcription	HSMMtube	muscle
20	chr1:192983200-192994400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:192983200-192995400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:192983200-192996400	Weak transcription	Fetal Stomach	stomach
23	chr1:192983200-193000000	Weak transcription	Right Ventricle	heart
24	chr1:192983200-193012800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:192983200-193018000	Weak transcription	Pancreas	Pancrea
26	chr1:192983200-193023600	Weak transcription	Psoas Muscle	Psoas
27	chr1:192983200-193027800	Weak transcription	Aorta	Aorta
28	chr1:192983800-192995400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:192984000-192994000	Weak transcription	NH-A	brain
30	chr1:192984000-192995000	Weak transcription	Osteobl	bone
31	chr1:192984000-192996200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:192984000-192997600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:192984000-192998200	Weak transcription	NHDF-Ad	bronchial
34	chr1:192984200-192994400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:192984200-193026600	Weak transcription	NHLF	lung
36	chr1:192984400-193026400	Weak transcription	HUVEC	blood vessel
37	chr1:192984800-193025800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:192986200-193012000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:192987000-193009200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:192987400-193026200	Weak transcription	Fetal Kidney	kidney
41	chr1:192987800-192994600	Weak transcription	Hela-S3	cervix
42	chr1:192988600-192997800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:192988600-193008400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:192988800-192997200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:192988800-192997400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:192988800-193006000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:192988800-193012600	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:192989000-192994400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:192989000-192998800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:192989200-192996600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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