Variant report

Variant	rs6664876
Chromosome Location	chr1:94333546-94333547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94332093..94333597-chr1:94363497..94365167,2	K562	blood:
2	chr1:94326500..94334861-chr1:94334949..94340833,11	K562	blood:
3	chr1:94329412..94331639-chr1:94331729..94334290,2	K562	blood:
4	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1051394	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165021	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165022	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165023	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165025	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165026	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12029548	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12029637	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12029670	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041975	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12758972	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2092698	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2092699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2103784	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2143992	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273165	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273166	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2391321	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3789459	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789460	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847191	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847193	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847263	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847264	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666633	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6667991	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6681169	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681265	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6684054	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697189	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6700244	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7364663	0.87[ASN][1000 genomes]
rs7367601	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7513489	0.82[ASN][1000 genomes]
rs7513786	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7514828	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7517632	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7518940	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555136	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7556047	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7556107	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6664876	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs6664876	RP11-488P3.1	cis	lung	GTEx
rs6664876	DNTTIP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94314200-94334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:94314200-94334400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:94322600-94334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:94328800-94334800	Weak transcription	Hela-S3	cervix
6	chr1:94329400-94334600	Weak transcription	A549	lung
7	chr1:94329600-94334000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:94329800-94335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:94330000-94333600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:94330000-94334200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:94330000-94334200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:94330000-94334600	Weak transcription	K562	blood
14	chr1:94330000-94337000	Weak transcription	Psoas Muscle	Psoas
15	chr1:94330000-94338800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:94330200-94334200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:94330200-94334600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:94330400-94334600	Weak transcription	HUVEC	blood vessel
19	chr1:94330600-94334200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:94330600-94334600	Weak transcription	HSMM	muscle
21	chr1:94330600-94335200	Weak transcription	NHLF	lung
22	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:94330800-94334000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:94330800-94334600	Weak transcription	Fetal Brain Male	brain
25	chr1:94330800-94334600	Weak transcription	Osteobl	bone
26	chr1:94330800-94336800	Weak transcription	Spleen	Spleen
27	chr1:94331000-94334000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:94331000-94334600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:94331000-94339000	Weak transcription	Pancreas	Pancrea
30	chr1:94331200-94334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:94331200-94334200	Weak transcription	Adipose Nuclei	Adipose
32	chr1:94331200-94334200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:94331200-94334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:94331400-94334200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:94331400-94334200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:94331400-94334200	Weak transcription	Aorta	Aorta
37	chr1:94331400-94334200	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:94331400-94334200	Weak transcription	Placenta	Placenta
39	chr1:94331400-94334200	Weak transcription	Gastric	stomach
40	chr1:94331400-94334200	Weak transcription	HMEC	breast
41	chr1:94331400-94334400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:94331400-94334400	Weak transcription	NH-A	brain
43	chr1:94331400-94334600	Weak transcription	Fetal Intestine Large	intestine
44	chr1:94331400-94335200	Weak transcription	Colonic Mucosa	Colon
45	chr1:94331600-94333800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:94331600-94334000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:94331600-94334200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:94331600-94334200	Weak transcription	Liver	Liver
49	chr1:94331600-94334400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:94331600-94334600	Weak transcription	Primary B cells from cord blood	blood

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