Variant report

Variant	rs3824987
Chromosome Location	chr11:108346103-108346104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:108344700..108347624-chr11:108347817..108350215,2	K562	blood:
2	chr11:108343327..108347067-chr11:108367096..108369729,3	K562	blood:
3	chr11:108336340..108338601-chr11:108345636..108347558,2	MCF-7	breast:
4	chr11:108344279..108347177-chr11:108367664..108370660,2	K562	blood:

Variant related genes	Relation type
ENSG00000166323	Chromatin interaction
ENSG00000178202	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10431061	1.00[CEU][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10749917	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10749918	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10789665	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10890834	0.82[CHD][hapmap]
rs10890848	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890849	0.84[ASN][1000 genomes]
rs11212617	0.84[CHD][hapmap]
rs11212636	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11212637	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11212638	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11212659	0.83[ASN][1000 genomes]
rs11212661	0.85[ASN][1000 genomes]
rs11212666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11212672	0.91[JPT][hapmap]
rs11212676	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]
rs12223381	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]
rs12419828	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12801988	0.81[ASN][1000 genomes]
rs186595	0.82[CHD][hapmap]
rs2118308	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2118309	0.82[JPT][hapmap]
rs227040	0.82[CHD][hapmap]
rs227041	0.82[CHD][hapmap]
rs227061	0.82[CHD][hapmap]
rs227068	0.82[CHD][hapmap]
rs227069	1.00[CEU][hapmap];0.93[CHD][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs227072	0.82[CHD][hapmap]
rs227073	0.86[ASW][hapmap];0.83[CHD][hapmap];0.95[YRI][hapmap]
rs227074	0.82[CHD][hapmap]
rs227077	0.82[CHD][hapmap]
rs227092	0.82[CHD][hapmap]
rs2356801	0.86[ASW][hapmap];0.84[CHD][hapmap];1.00[YRI][hapmap]
rs3765632	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3901851	0.84[ASN][1000 genomes]
rs419716	0.82[CHD][hapmap]
rs4585	0.82[CHD][hapmap]
rs4753842	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4754322	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs573890	0.81[CHD][hapmap]
rs599558	0.82[CHD][hapmap]
rs60639858	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs611646	1.00[CEU][hapmap]
rs61913892	0.83[ASN][1000 genomes]
rs619972	0.86[ASW][hapmap];0.82[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs620613	0.95[YRI][hapmap]
rs652311	0.82[CHD][hapmap]
rs6589018	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7111091	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7126588	0.84[ASN][1000 genomes]
rs751343	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7931930	0.93[CHD][hapmap]
rs7934719	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7943063	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7943203	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs893279	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3824987	KDELC2	cis	Esophagus Mucosa	GTEx
rs3824987	NPAT	cis	cerebellum	SCAN
rs3824987	AVIL	trans	parietal	SCAN
rs3824987	ACAT1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108338200-108346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:108338200-108359000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:108338200-108367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:108338400-108347600	Weak transcription	Lung	lung
5	chr11:108338400-108352600	Weak transcription	Spleen	Spleen
6	chr11:108338600-108347800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:108338600-108364800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:108338600-108367200	Weak transcription	A549	lung
9	chr11:108338600-108367800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:108338800-108347200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:108338800-108347400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:108338800-108347400	Weak transcription	Fetal Kidney	kidney
13	chr11:108338800-108347400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:108338800-108347600	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:108338800-108347600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:108338800-108347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:108338800-108347800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:108338800-108347800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:108338800-108347800	Weak transcription	Colonic Mucosa	Colon
20	chr11:108338800-108347800	Weak transcription	Left Ventricle	heart
21	chr11:108338800-108347800	Weak transcription	Right Ventricle	heart
22	chr11:108338800-108348200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:108338800-108349000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:108338800-108352400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:108338800-108354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:108338800-108356800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:108338800-108356800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:108338800-108356800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:108338800-108357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:108338800-108367200	Weak transcription	HSMMtube	muscle
31	chr11:108338800-108367400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:108338800-108367400	Weak transcription	HUVEC	blood vessel
33	chr11:108338800-108367600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:108338800-108367600	Weak transcription	Small Intestine	intestine
35	chr11:108338800-108368000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:108339000-108346600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:108339000-108347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:108339000-108348000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:108339000-108356800	Weak transcription	Brain Germinal Matrix	brain
40	chr11:108339000-108359000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:108339000-108367200	Weak transcription	NHEK	skin
42	chr11:108339000-108367400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:108339000-108368000	Weak transcription	Primary B cells from cord blood	blood
44	chr11:108339000-108368000	Weak transcription	Fetal Brain Female	brain
45	chr11:108339200-108347400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr11:108339200-108347600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:108339200-108347600	Weak transcription	Brain Anterior Caudate	brain
48	chr11:108339200-108348000	Weak transcription	NHDF-Ad	bronchial
49	chr11:108339200-108348800	Weak transcription	Hela-S3	cervix
50	chr11:108339200-108352400	Weak transcription	K562	blood

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