Variant report

Variant	rs11234102
Chromosome Location	chr11:71255125-71255126
allele	A/C
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	chr11:71254974-71255406	HL-60	blood:	n/a	n/a
2	RUNX3	chr11:71254913-71255255	GM12878	blood:	n/a	n/a
3	SPI1	chr11:71254924-71255406	HL-60	blood:	n/a	n/a
4	EGR1	chr11:71255055-71255243	K562	blood:	n/a	n/a
5	MAX	chr11:71254915-71255305	NB4	blood:	n/a	chr11:71255095-71255106 chr11:71255092-71255107 chr11:71255096-71255103
6	EGR1	chr11:71255006-71255226	K562	blood:	n/a	n/a
7	RUNX3	chr11:71254930-71255211	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:71254920-71255340	HL-60	blood:	n/a	n/a
9	MYC	chr11:71254914-71255326	NB4	blood:	n/a	chr11:71255095-71255106 chr11:71255092-71255107 chr11:71255096-71255103
10	BHLHE40	chr11:71254944-71255240	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71254168..71255682-chr11:71257713..71259935,2	MCF-7	breast:
2	chr11:71253515..71257343-chr11:71260479..71262893,3	MCF-7	breast:

Variant related genes	Relation type
KRTAP5-9	TF binding region
ENSG00000254997	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10751114	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792762	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792763	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792770	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10792776	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792777	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792778	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792779	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10898254	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898255	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10898256	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10898261	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898282	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898286	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898288	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898289	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898290	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10898293	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234143	0.84[EUR][1000 genomes]
rs11234148	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234149	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600364	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604725	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11605448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606159	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12792437	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2663	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762929	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35647583	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4129753	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4129754	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945017	0.83[ASN][1000 genomes]
rs55921335	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6592186	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6592187	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6592188	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6592189	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6592190	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67152879	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67293913	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67450797	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68163405	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7125610	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7126613	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128806	0.88[CEU][hapmap]
rs72958323	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7358341	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7395845	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7926544	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7926576	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7926656	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938628	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7941700	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7943893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949169	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv468632	chr11:71200320-71289089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv555402	chr11:71200320-71289089	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3372246	chr11:71223101-71435819	Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897900	chr11:71234107-71276909	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv897899	chr11:71234107-71277981	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv3363568	chr11:71237277-71275754	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3425891	chr11:71237287-71275790	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv3528100	chr11:71237332-71275725	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv3528101	chr11:71237332-71275725	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	esv3432021	chr11:71237346-71275760	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11234102	KRTAP5-9	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71232800-71259800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:71251200-71255400	ZNF genes & repeats	GM12878-XiMat	blood
3	chr11:71252800-71257000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:71252800-71257000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr11:71254000-71255200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr11:71254000-71256200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:71254200-71255200	Enhancers	Primary B cells from cord blood	blood
8	chr11:71254200-71255200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr11:71254200-71256200	Enhancers	Primary hematopoietic stem cells	blood
10	chr11:71254200-71256400	Enhancers	HepG2	liver
11	chr11:71254200-71256600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:71254400-71255200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr11:71254400-71255400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr11:71254400-71255400	Enhancers	Primary B cells from peripheral blood	blood
15	chr11:71254600-71255400	Enhancers	Fetal Thymus	thymus
16	chr11:71254800-71255200	Enhancers	Stomach Mucosa	stomach
17	chr11:71254800-71255400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:71254800-71256400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr11:71255000-71255200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:71255000-71255200	Enhancers	Left Ventricle	heart
21	chr11:71255000-71255200	Bivalent Enhancer	Small Intestine	intestine
22	chr11:71255000-71255400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:71255000-71255400	Enhancers	Fetal Intestine Large	intestine
24	chr11:71255000-71255600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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