Variant report

Variant	rs11769054
Chromosome Location	chr7:7811461-7811462
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	POLR2A	chr7:7811377-7811461	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7804210..7807179-chr7:7808630..7811509,2	MCF-7	breast:
2	chr7:7809766..7812689-chr7:8007861..8010451,3	MCF-7	breast:

Variant related genes	Relation type
RPA3-AS1	TF binding region
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11764567	0.84[CHB][hapmap]
rs11768218	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11771147	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12702644	0.88[ASN][1000 genomes]
rs12702646	0.86[ASN][1000 genomes]
rs13221072	0.84[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs13221076	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs35023386	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36005831	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1026564	chr7:7734846-7897847	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv887489	chr7:7770203-7913311	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1027770	chr7:7797431-7957507	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv538722	chr7:7797431-7957507	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv887490	chr7:7801684-7908970	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11769054	KDELR2	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7802400-7812000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:7802400-7812000	Weak transcription	Brain Substantia Nigra	brain
3	chr7:7802400-7812200	Weak transcription	Small Intestine	intestine
4	chr7:7802400-7829800	Weak transcription	Left Ventricle	heart
5	chr7:7802400-7841400	Weak transcription	Ovary	ovary
6	chr7:7802600-7811800	Weak transcription	Brain Anterior Caudate	brain
7	chr7:7802600-7812200	Weak transcription	Adipose Nuclei	Adipose
8	chr7:7802600-7836600	Weak transcription	Aorta	Aorta
9	chr7:7804600-7811800	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:7804800-7811600	Weak transcription	Primary B cells from cord blood	blood
11	chr7:7805400-7811800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:7805400-7854400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr7:7805800-7811600	Weak transcription	GM12878-XiMat	blood
14	chr7:7807600-7819000	Weak transcription	Stomach Mucosa	stomach
15	chr7:7808000-7812000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:7808000-7813600	Weak transcription	Hela-S3	cervix
17	chr7:7808800-7811800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:7808800-7811800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:7808800-7811800	Weak transcription	HSMMtube	muscle
20	chr7:7809000-7811800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:7809200-7811800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:7809400-7812000	Enhancers	Osteobl	bone
23	chr7:7809400-7812200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:7809400-7813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:7810000-7811800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:7810200-7811800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:7810200-7812000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:7810200-7812000	Weak transcription	Fetal Stomach	stomach
29	chr7:7810200-7812000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:7810200-7813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:7810800-7811600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:7810800-7811600	Enhancers	Thymus	Thymus
33	chr7:7810800-7811800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr7:7810800-7811800	Weak transcription	Brain Germinal Matrix	brain
35	chr7:7810800-7811800	Enhancers	HMEC	breast
36	chr7:7810800-7812000	Enhancers	Primary T cells from cord blood	blood
37	chr7:7810800-7812000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:7810800-7812200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr7:7810800-7812600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:7811000-7811800	Enhancers	NHEK	skin
41	chr7:7811000-7812000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:7811000-7812000	Enhancers	HSMM	muscle
43	chr7:7811000-7812600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:7811000-7812800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:7811200-7811600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:7811200-7811800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr7:7811200-7811800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:7811200-7812000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:7811200-7812000	Enhancers	NH-A	brain
50	chr7:7811400-7811600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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