Variant report

Variant	rs12223381
Chromosome Location	chr11:108354102-108354103
allele	C/T
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	FOS	chr11:108353946-108354316	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr11:108353989-108354279	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr11:108353977-108354279	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr11:108353849-108354297	T-47D	breast:	n/a	n/a
5	FOXA1	chr11:108353923-108354155	T-47D	breast:	n/a	n/a
6	STAT3	chr11:108353514-108354123	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr11:108353942-108354110	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA1	chr11:108353943-108354166	T-47D	breast:	n/a	n/a
9	MYC	chr11:108353930-108354186	MCF10A-Er-Src	breast:	n/a	n/a
10	JUND	chr11:108354019-108354254	HepG2	liver:	n/a	chr11:108354129-108354140
11	EP300	chr11:108353802-108354364	T-47D	breast:	n/a	n/a
12	FOS	chr11:108353953-108354294	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108351170..108356197-chr11:108366781..108370741,5	K562	blood:

Variant related genes	Relation type
KDELC2	TF binding region
ENSG00000178202	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10431061	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10749917	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10749918	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10789665	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890834	0.93[YRI][hapmap]
rs10890848	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10890849	0.90[ASN][1000 genomes]
rs11212636	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11212637	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11212638	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11212659	0.89[ASN][1000 genomes]
rs11212661	0.89[ASN][1000 genomes]
rs11212666	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11212672	0.91[JPT][hapmap]
rs11212676	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs113995	0.90[YRI][hapmap]
rs12419828	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12801988	0.88[ASN][1000 genomes]
rs186593	0.90[YRI][hapmap]
rs186595	0.93[YRI][hapmap]
rs2118308	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2118309	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs227040	0.93[YRI][hapmap]
rs227058	0.87[YRI][hapmap]
rs227062	0.93[YRI][hapmap]
rs227069	1.00[CEU][hapmap]
rs227072	0.93[YRI][hapmap]
rs227074	0.93[YRI][hapmap]
rs227077	0.93[YRI][hapmap]
rs227087	0.93[YRI][hapmap]
rs3765632	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3824987	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3901851	0.91[ASN][1000 genomes]
rs4585	0.96[YRI][hapmap]
rs4753842	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4754322	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs573890	0.93[YRI][hapmap]
rs599558	0.89[YRI][hapmap]
rs60639858	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs611646	1.00[CEU][hapmap]
rs61913892	0.89[ASN][1000 genomes]
rs645485	0.89[YRI][hapmap]
rs652311	0.93[YRI][hapmap]
rs654005	0.87[YRI][hapmap]
rs6589018	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs662578	0.90[YRI][hapmap]
rs7111091	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7126588	0.88[ASN][1000 genomes]
rs751343	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934719	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7943063	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7943203	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs893279	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12223381	KDELC2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108338200-108359000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:108338200-108367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:108338600-108364800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:108338600-108367200	Weak transcription	A549	lung
5	chr11:108338600-108367800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:108338800-108354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:108338800-108356800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:108338800-108356800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:108338800-108356800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:108338800-108357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:108338800-108367200	Weak transcription	HSMMtube	muscle
12	chr11:108338800-108367400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:108338800-108367400	Weak transcription	HUVEC	blood vessel
14	chr11:108338800-108367600	Weak transcription	Brain Angular Gyrus	brain
15	chr11:108338800-108367600	Weak transcription	Small Intestine	intestine
16	chr11:108338800-108368000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:108339000-108356800	Weak transcription	Brain Germinal Matrix	brain
18	chr11:108339000-108359000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:108339000-108367200	Weak transcription	NHEK	skin
20	chr11:108339000-108367400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr11:108339000-108368000	Weak transcription	Primary B cells from cord blood	blood
22	chr11:108339000-108368000	Weak transcription	Fetal Brain Female	brain
23	chr11:108339200-108363000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:108339200-108367400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:108339200-108367600	Weak transcription	Brain Hippocampus Middle	brain
26	chr11:108339200-108367800	Weak transcription	Fetal Brain Male	brain
27	chr11:108339200-108368000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:108343000-108361800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:108344000-108361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:108344000-108362000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:108344000-108363000	Strong transcription	Dnd41	blood
32	chr11:108344200-108357600	Strong transcription	Adipose Nuclei	Adipose
33	chr11:108344200-108361800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:108344200-108362000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:108344600-108361000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr11:108344800-108357200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:108345000-108358200	Strong transcription	Primary T cells from cord blood	blood
38	chr11:108345400-108355200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:108345800-108355000	Weak transcription	Pancreas	Pancrea
40	chr11:108345800-108359000	Weak transcription	Gastric	stomach
41	chr11:108346000-108364800	Weak transcription	Fetal Heart	heart
42	chr11:108346000-108367200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr11:108346000-108367600	Weak transcription	Brain Substantia Nigra	brain
44	chr11:108346200-108357000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:108347200-108358200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:108347400-108361800	Strong transcription	Liver	Liver
47	chr11:108347800-108354800	Weak transcription	NHLF	lung
48	chr11:108348400-108354600	Weak transcription	Fetal Intestine Small	intestine
49	chr11:108348400-108355000	Weak transcription	Lung	lung
50	chr11:108348400-108364800	Weak transcription	Colon Smooth Muscle	Colon

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