Variant report

Variant	rs11212676
Chromosome Location	chr11:108361578-108361579
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	FOXA1	chr11:108361545-108361762	T-47D	breast:	n/a	chr11:108361588-108361600
2	FOXA1	chr11:108361454-108361720	HepG2	liver:	n/a	chr11:108361588-108361600
3	FOXA1	chr11:108361264-108361692	T-47D	breast:	n/a	chr11:108361588-108361600
4	GATA3	chr11:108361294-108361749	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108332946..108340923-chr11:108359972..108371658,26	K562	blood:
2	chr11:108333954..108342521-chr11:108361561..108373383,35	K562	blood:

Variant related genes	Relation type
KDELC2	TF binding region
ENSG00000166323	Chromatin interaction
ENSG00000221607	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10431061	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10749917	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10749918	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10789665	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10890848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890849	0.85[ASN][1000 genomes]
rs11212636	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11212637	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11212638	0.92[EUR][1000 genomes]
rs11212666	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11212672	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12223381	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]
rs12419828	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12801988	0.81[ASN][1000 genomes]
rs2118308	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs227069	0.91[CEU][hapmap];0.83[MEX][hapmap]
rs3765632	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs3824987	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4753842	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4754322	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60639858	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs611646	0.91[CEU][hapmap]
rs6589018	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7111091	0.89[EUR][1000 genomes]
rs751343	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7934719	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7943063	0.91[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7943203	0.91[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs893279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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
rs11212676	KDELC2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108338200-108367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:108338600-108364800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:108338600-108367200	Weak transcription	A549	lung
4	chr11:108338600-108367800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:108338800-108367200	Weak transcription	HSMMtube	muscle
6	chr11:108338800-108367400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:108338800-108367400	Weak transcription	HUVEC	blood vessel
8	chr11:108338800-108367600	Weak transcription	Brain Angular Gyrus	brain
9	chr11:108338800-108367600	Weak transcription	Small Intestine	intestine
10	chr11:108338800-108368000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:108339000-108367200	Weak transcription	NHEK	skin
12	chr11:108339000-108367400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:108339000-108368000	Weak transcription	Primary B cells from cord blood	blood
14	chr11:108339000-108368000	Weak transcription	Fetal Brain Female	brain
15	chr11:108339200-108363000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:108339200-108367400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:108339200-108367600	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:108339200-108367800	Weak transcription	Fetal Brain Male	brain
19	chr11:108339200-108368000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:108343000-108361800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:108344000-108361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:108344000-108362000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:108344000-108363000	Strong transcription	Dnd41	blood
24	chr11:108344200-108361800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:108344200-108362000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:108346000-108364800	Weak transcription	Fetal Heart	heart
27	chr11:108346000-108367200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:108346000-108367600	Weak transcription	Brain Substantia Nigra	brain
29	chr11:108347400-108361800	Strong transcription	Liver	Liver
30	chr11:108348400-108364800	Weak transcription	Colon Smooth Muscle	Colon
31	chr11:108348400-108367400	Weak transcription	Colonic Mucosa	Colon
32	chr11:108348400-108367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:108348600-108367200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:108348600-108367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:108348600-108367400	Weak transcription	Esophagus	oesophagus
36	chr11:108348600-108367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:108348800-108367600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr11:108349200-108367200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:108350000-108367400	Weak transcription	Hela-S3	cervix
40	chr11:108350200-108367400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:108350200-108367400	Weak transcription	Fetal Kidney	kidney
42	chr11:108350400-108367400	Weak transcription	Brain Anterior Caudate	brain
43	chr11:108350800-108362000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:108351400-108362000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:108352000-108362000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:108352400-108361800	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:108352400-108362400	Strong transcription	Fetal Stomach	stomach
48	chr11:108353000-108367800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:108353400-108367400	Weak transcription	Spleen	Spleen
50	chr11:108353800-108367400	Weak transcription	Rectal Mucosa Donor 31	rectum

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