Variant report

Variant	rs7543502
Chromosome Location	chr1:174653701-174653702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10489261	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs16847121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs16847206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16847237	0.84[CHD][hapmap]
rs2179108	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2179109	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2901819	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41266052	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs41397546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4515855	0.85[EUR][1000 genomes]
rs56864802	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57053120	0.81[EUR][1000 genomes]
rs57132183	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs57243929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57648142	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57898822	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58063264	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs58762254	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59190079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59262554	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs59354288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59436654	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60240702	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60665754	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60723087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60865584	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60885521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61028529	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61329817	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6673649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6692753	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6695956	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703536	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7543502		cis	Lymphoblastoid	GTEx
rs7543502	CRYM	trans	lymphoblastoid	RTeQTL
rs7543502	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs7543502	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174607600-174677800	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174646800-174677600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:174646800-174680400	Weak transcription	Ovary	ovary
4	chr1:174648000-174660400	Weak transcription	Esophagus	oesophagus
5	chr1:174648400-174665200	Weak transcription	Left Ventricle	heart
6	chr1:174649200-174668400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:174651200-174664600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:174651400-174665200	Weak transcription	Lung	lung
9	chr1:174651600-174657800	Weak transcription	Adipose Nuclei	Adipose
10	chr1:174651800-174673000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:174651800-174677400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:174652000-174656800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:174652000-174660200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:174652200-174656800	Weak transcription	Fetal Lung	lung
15	chr1:174652200-174657600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:174652200-174658600	Weak transcription	Fetal Intestine Small	intestine
17	chr1:174652400-174677400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:174652400-174678800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:174652600-174657600	Weak transcription	HepG2	liver
20	chr1:174653000-174653800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:174653200-174655600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:174653400-174654400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:174653400-174654400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:174653400-174657000	Strong transcription	GM12878-XiMat	blood

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