Variant report

Variant	rs7943820
Chromosome Location	chr11:108389285-108389286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:108367577..108369430-chr11:108387376..108390021,2	K562	blood:
2	chr11:108367494..108369928-chr11:108388212..108391402,3	MCF-7	breast:
3	chr11:108357774..108359460-chr11:108388909..108390796,2	K562	blood:
4	chr11:108367272..108370031-chr11:108388462..108390662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178202	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10431062	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12361570	0.82[JPT][hapmap]
rs2846412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7116971	0.85[YRI][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7943820	GRIA4	cis	cerebellum	SCAN
rs7943820	KDELC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108370400-108408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:108371800-108406400	Weak transcription	Gastric	stomach
3	chr11:108372000-108401200	Weak transcription	Esophagus	oesophagus
4	chr11:108381000-108408800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr11:108382000-108396000	Weak transcription	Pancreas	Pancrea
6	chr11:108383000-108398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:108384000-108390600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:108384800-108393000	Weak transcription	GM12878-XiMat	blood
9	chr11:108385000-108389600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:108385000-108409000	Weak transcription	Fetal Kidney	kidney
11	chr11:108385000-108414000	Weak transcription	HSMM	muscle
12	chr11:108385000-108422800	Weak transcription	Fetal Intestine Small	intestine
13	chr11:108385200-108396200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:108385200-108403600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:108385400-108389800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:108385400-108391800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:108385400-108394800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:108385400-108395600	Weak transcription	Lung	lung
19	chr11:108385400-108409200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:108385600-108389800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:108385600-108390400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:108385600-108391000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr11:108385600-108392000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:108385600-108396000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:108385600-108396400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:108385600-108397000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:108385600-108397000	Weak transcription	K562	blood
28	chr11:108385600-108402600	Weak transcription	Brain Anterior Caudate	brain
29	chr11:108385600-108405000	Weak transcription	HMEC	breast
30	chr11:108385600-108405200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:108385600-108408400	Weak transcription	Aorta	Aorta
32	chr11:108385600-108408800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:108385600-108409400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:108385600-108412400	Weak transcription	HSMMtube	muscle
35	chr11:108387000-108390400	Strong transcription	Liver	Liver
36	chr11:108387600-108394400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:108388600-108389600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:108389000-108390200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:108389200-108389400	Weak transcription	Placenta	Placenta
40	chr11:108389200-108394800	Weak transcription	NHEK	skin

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