Variant report

Variant	rs12535238
Chromosome Location	chr7:128345523-128345524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128343789..128345525-chr7:128387632..128390357,2	K562	blood:
2	chr7:128336358..128338918-chr7:128343519..128346350,2	K562	blood:
3	chr7:128343745..128346373-chr7:128352660..128354319,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201041	Chromatin interaction
ENSG00000252866	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10085435	0.81[EUR][1000 genomes]
rs10224862	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233059	0.82[EUR][1000 genomes]
rs10241185	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10242806	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253131	0.84[EUR][1000 genomes]
rs10259359	0.80[EUR][1000 genomes]
rs10270431	0.84[EUR][1000 genomes]
rs10270985	0.87[EUR][1000 genomes]
rs10274878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10276810	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10954205	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11761312	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766319	0.82[AMR][1000 genomes]
rs11768485	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12333625	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12536288	0.89[ASN][1000 genomes]
rs12706858	1.00[ASN][1000 genomes]
rs13224613	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13233377	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235219	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13237593	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521711	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs339070	1.00[ASN][1000 genomes]
rs339071	1.00[ASN][1000 genomes]
rs339074	1.00[ASN][1000 genomes]
rs339079	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339093	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34120723	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34490491	0.84[EUR][1000 genomes]
rs34751214	0.84[EUR][1000 genomes]
rs35247963	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35336068	0.86[AFR][1000 genomes]
rs35825132	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35871589	0.85[EUR][1000 genomes]
rs3816421	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4289745	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467201	0.84[EUR][1000 genomes]
rs6467205	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6943737	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946179	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954329	0.88[AFR][1000 genomes]
rs6960296	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6961754	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6967393	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6971819	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6972787	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976879	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977126	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71548762	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776915	0.81[EUR][1000 genomes]
rs7778731	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7787764	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7790478	1.00[ASN][1000 genomes]
rs7804472	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7810047	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811083	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9690934	0.84[EUR][1000 genomes]
rs9692416	0.84[EUR][1000 genomes]
rs9768808	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9769753	0.84[EUR][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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12535238	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs12535238	CICP14	cis	Esophagus Mucosa	GTEx
rs12535238	CICP14	cis	Thyroid	GTEx
rs12535238	CICP14	cis	lung	GTEx
rs12535238	CICP14	cis	Esophagus Muscularis	GTEx
rs12535238	METTL2B	cis	Artery Tibial	GTEx
rs12535238	CICP14	cis	Muscle Skeletal	GTEx
rs12535238	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs12535238	CICP14	cis	Nerve Tibial	GTEx
rs12535238	RP11-274B21.10	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128338000-128346000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:128338600-128349000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:128339000-128358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:128341200-128346000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:128341800-128346000	Weak transcription	HMEC	breast
6	chr7:128343600-128345600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:128343800-128345800	Weak transcription	Right Atrium	heart
8	chr7:128344000-128346200	Weak transcription	Spleen	Spleen
9	chr7:128344000-128348200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:128344000-128349000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:128344200-128348600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:128344400-128348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:128344600-128347000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:128344800-128346400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:128344800-128346400	Bivalent Enhancer	K562	blood
16	chr7:128345000-128345600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:128345000-128346000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:128345200-128345600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr7:128345200-128350200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:128345200-128350200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr7:128345400-128348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:128345400-128348000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:128345400-128348400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:128345400-128348600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:128345400-128348600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr7:128345400-128348800	Weak transcription	H1 Cell Line	embryonic stem cell

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