Variant report

Variant	rs17110225
Chromosome Location	chr1:94118883-94118884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94118762-94121779	Hela-S3	cervix:	n/a	n/a
2	FAM48A	chr1:94118818-94118972	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:94118754-94121235	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:94118032-94121009	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94118755..94120990-chr1:94126117..94127975,2	K562	blood:
2	chr1:94117141..94121029-chr1:94132853..94136106,3	K562	blood:

Variant related genes	Relation type
BCAR3	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	1.00[ASN][1000 genomes]
rs11579004	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11579685	1.00[ASN][1000 genomes]
rs11580965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588860	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12066343	1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs12732557	1.00[ASN][1000 genomes]
rs12739747	0.90[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12740779	1.00[ASN][1000 genomes]
rs12744941	1.00[ASN][1000 genomes]
rs12757325	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12760092	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17110063	1.00[ASN][1000 genomes]
rs17110101	1.00[ASN][1000 genomes]
rs17110111	1.00[ASN][1000 genomes]
rs17110179	0.85[AMR][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877604	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34423897	1.00[ASN][1000 genomes]
rs34663884	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34666525	1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	1.00[ASN][1000 genomes]
rs35972761	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36115605	1.00[ASN][1000 genomes]
rs3950119	1.00[ASN][1000 genomes]
rs59996315	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61780979	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61780999	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6683296	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66966060	1.00[ASN][1000 genomes]
rs67043929	1.00[ASN][1000 genomes]
rs67300695	1.00[ASN][1000 genomes]
rs67354439	1.00[ASN][1000 genomes]
rs67511232	1.00[ASN][1000 genomes]
rs71652539	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72721041	1.00[ASN][1000 genomes]
rs7511890	1.00[ASN][1000 genomes]
rs7525880	1.00[ASN][1000 genomes]
rs7531106	1.00[ASN][1000 genomes]
rs7543098	1.00[ASN][1000 genomes]
rs7543763	1.00[ASN][1000 genomes]
rs7553185	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7555302	1.00[ASN][1000 genomes]
rs761802	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17110225	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs17110225	TMEM56	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94094200-94120400	Weak transcription	Psoas Muscle	Psoas
2	chr1:94095600-94125400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:94100000-94135800	Weak transcription	Fetal Stomach	stomach
4	chr1:94101600-94128800	Weak transcription	Right Ventricle	heart
5	chr1:94102000-94119800	Weak transcription	HSMMtube	muscle
6	chr1:94102000-94125400	Weak transcription	Fetal Kidney	kidney
7	chr1:94102000-94125600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:94102600-94119200	Weak transcription	Fetal Intestine Small	intestine
9	chr1:94102800-94119000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:94103000-94121800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:94103800-94135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:94106400-94126000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:94107200-94125600	Weak transcription	Aorta	Aorta
14	chr1:94107600-94119200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:94107800-94120000	Weak transcription	Primary B cells from cord blood	blood
16	chr1:94108200-94119400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:94108400-94119000	Weak transcription	Adipose Nuclei	Adipose
18	chr1:94108400-94119200	Weak transcription	NHLF	lung
19	chr1:94108600-94122200	Weak transcription	HUVEC	blood vessel
20	chr1:94108600-94130400	Weak transcription	Esophagus	oesophagus
21	chr1:94110000-94119200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:94110200-94124400	Strong transcription	NHEK	skin
23	chr1:94110800-94120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:94110800-94127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:94110800-94128800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:94110800-94130200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:94111200-94127600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:94111600-94126800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:94111800-94122200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:94111800-94127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:94112400-94119000	Strong transcription	HSMM	muscle
32	chr1:94112400-94125800	Strong transcription	Hela-S3	cervix
33	chr1:94112400-94127400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:94113000-94122400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:94113800-94124200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:94114600-94125600	Weak transcription	Brain Substantia Nigra	brain
37	chr1:94114800-94119200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:94114800-94120200	Strong transcription	HMEC	breast
39	chr1:94115000-94119200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:94115000-94128800	Weak transcription	Left Ventricle	heart
41	chr1:94115000-94132000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:94116000-94120200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:94116400-94120800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:94116800-94120800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:94117200-94119400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:94117200-94119400	Enhancers	Ovary	ovary
47	chr1:94117200-94119800	Weak transcription	Osteobl	bone
48	chr1:94117200-94121000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:94117400-94120800	Strong transcription	Placenta	Placenta
50	chr1:94117400-94127400	Genic enhancers	Muscle Satellite Cultured Cells	--

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