Variant report

Variant	rs6660210
Chromosome Location	chr1:94304926-94304927
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	chr1:94303067..94305245-chr1:94310697..94313072,2	K562	blood:
2	chr1:94302532..94305136-chr1:94310804..94313101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10874797	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164970	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164973	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11165022	0.82[CEU][hapmap]
rs11582870	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12097812	0.81[EUR][1000 genomes]
rs1884019	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1980083	0.85[CHB][hapmap]
rs2092700	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143991	0.80[ASN][1000 genomes]
rs2235970	0.84[JPT][hapmap]
rs2301022	0.94[JPT][hapmap]
rs2391315	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2391321	0.85[CEU][hapmap]
rs2747036	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747037	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2747038	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2747040	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2747042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747044	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747047	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2747049	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2818161	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2818165	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2818166	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2818167	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789453	0.83[GIH][hapmap];0.94[JPT][hapmap]
rs3789457	1.00[JPT][hapmap]
rs4520428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4847184	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4847192	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847254	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4847257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541399	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681265	0.81[CEU][hapmap]
rs6703684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743110	0.86[GIH][hapmap];0.94[JPT][hapmap]
rs7523787	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7526082	0.85[ASN][1000 genomes]
rs7552293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947343	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][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	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6660210	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs6660210	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs6660210	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs6660210	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs6660210	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94283400-94310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:94284200-94306200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:94284200-94311200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:94290200-94311400	Weak transcription	Aorta	Aorta
5	chr1:94294200-94305400	Weak transcription	A549	lung
6	chr1:94295400-94310000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:94298200-94307000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:94298800-94305000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:94299000-94308600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:94299400-94310200	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:94300600-94309400	Weak transcription	Dnd41	blood
12	chr1:94300800-94311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:94301400-94309600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:94302000-94305000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:94302200-94309600	Weak transcription	Placenta	Placenta
16	chr1:94302200-94311200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:94302200-94311200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:94302800-94309600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:94303000-94305800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:94303200-94309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:94303200-94310200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:94303800-94306000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:94303800-94306800	Weak transcription	Spleen	Spleen
24	chr1:94303800-94311600	Weak transcription	Gastric	stomach
25	chr1:94304000-94311200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:94304200-94311000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:94304400-94305800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:94304400-94305800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr1:94304400-94306000	Enhancers	NHDF-Ad	bronchial
30	chr1:94304400-94306200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:94304400-94310200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:94304600-94305800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:94304600-94306400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:94304800-94305200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:94304800-94305600	Enhancers	NHEK	skin
36	chr1:94304800-94305800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:94304800-94305800	Enhancers	NH-A	brain
38	chr1:94304800-94306200	Enhancers	HMEC	breast
39	chr1:94304800-94306400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:94304800-94306400	Enhancers	NHLF	lung
41	chr1:94304800-94307000	Enhancers	Hela-S3	cervix

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