Variant report

Variant	rs17304770
Chromosome Location	chr1:94282287-94282288
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	chr1:94145260..94147356-chr1:94280674..94282798,2	MCF-7	breast:
2	chr1:94280000..94282465-chr1:94282888..94285001,2	K562	blood:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10489605	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs10874795	0.97[ASN][1000 genomes]
rs1108527	0.81[EUR][1000 genomes]
rs1108528	0.86[EUR][1000 genomes]
rs11164994	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165001	0.91[ASN][1000 genomes]
rs11165019	0.97[ASN][1000 genomes]
rs12076307	1.00[CHB][hapmap]
rs12079584	0.97[ASN][1000 genomes]
rs12239830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467129	0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17100397	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110408	0.91[ASN][1000 genomes]
rs17878271	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17878294	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17881810	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17884788	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17885151	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17886352	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1877605	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2223908	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761913	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41292665	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4526623	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs4615846	0.82[ASN][1000 genomes]
rs57870303	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61425457	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781048	0.85[EUR][1000 genomes]
rs61781049	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61781051	1.00[EUR][1000 genomes]
rs61781053	0.98[EUR][1000 genomes]
rs61781054	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781055	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781056	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781057	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782162	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782163	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782164	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782165	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782398	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782399	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782400	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782403	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782404	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782405	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782410	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782413	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782449	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61782450	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782451	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782458	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782459	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6541394	1.00[CHB][hapmap]
rs6660794	0.91[ASN][1000 genomes]
rs6671839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6674149	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689215	0.89[ASN][1000 genomes]
rs6689746	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs6703468	0.91[ASN][1000 genomes]
rs717913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs72723114	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723118	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723125	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723138	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723157	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723165	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723169	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723178	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72967397	0.97[ASN][1000 genomes]
rs7523682	0.94[EUR][1000 genomes]
rs871436	0.82[CEU][hapmap];1.00[GIH][hapmap]

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	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	esv1005153	chr1:94281705-94283362	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17304770	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94273600-94282800	Weak transcription	Lung	lung
2	chr1:94275800-94282400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
4	chr1:94275800-94285000	Enhancers	HMEC	breast
5	chr1:94276000-94283600	Enhancers	HSMM	muscle
6	chr1:94276000-94285200	Enhancers	Placenta	Placenta
7	chr1:94276800-94283800	Enhancers	NHEK	skin
8	chr1:94277000-94282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:94277000-94284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:94277000-94285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:94277200-94282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:94277600-94284600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:94277800-94282600	Weak transcription	Fetal Stomach	stomach
14	chr1:94278200-94282600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:94278200-94282800	Weak transcription	Right Ventricle	heart
16	chr1:94278600-94283200	Enhancers	Osteobl	bone
17	chr1:94278600-94284000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:94278800-94282600	Weak transcription	Left Ventricle	heart
19	chr1:94279400-94282400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:94279400-94282800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:94279400-94284400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:94279600-94282400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:94279600-94282400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:94279600-94282400	Weak transcription	Fetal Intestine Small	intestine
25	chr1:94279600-94282400	Weak transcription	NHDF-Ad	bronchial
26	chr1:94279600-94282600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:94279800-94282400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:94279800-94282400	Weak transcription	HepG2	liver
30	chr1:94279800-94282600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:94279800-94282600	Weak transcription	NHLF	lung
32	chr1:94279800-94284400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:94279800-94284600	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:94280000-94282400	Weak transcription	Liver	Liver
35	chr1:94280000-94282400	Weak transcription	Fetal Thymus	thymus
36	chr1:94280000-94282600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:94280000-94282800	Weak transcription	Fetal Intestine Large	intestine
38	chr1:94280000-94285600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:94280000-94290000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:94280200-94282400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:94280200-94282400	Weak transcription	Right Atrium	heart
42	chr1:94280200-94284000	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:94280400-94282800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr1:94280400-94285000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:94280600-94282400	Enhancers	HUVEC	blood vessel
46	chr1:94280800-94282800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:94280800-94283200	Enhancers	HSMMtube	muscle
48	chr1:94280800-94283400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:94280800-94285800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:94281000-94282600	Weak transcription	Fetal Muscle Leg	muscle

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