Variant report

Variant	rs896693
Chromosome Location	chr11:120067082-120067083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120064484..120070047-chr11:120078272..120084162,6	MCF-7	breast:
2	chr11:120066886..120069148-chr11:120079541..120081080,2	K562	blood:

Variant related genes	Relation type
ENSG00000184232	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10790369	0.83[JPT][hapmap]
rs10892547	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11217705	0.85[JPT][hapmap]
rs11217732	0.84[JPT][hapmap]
rs11217739	0.85[JPT][hapmap]
rs11217742	0.85[JPT][hapmap]
rs11217748	0.85[JPT][hapmap]
rs11217749	0.85[JPT][hapmap]
rs11217750	0.83[JPT][hapmap]
rs12049837	0.83[JPT][hapmap]
rs12273399	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12278345	0.91[EUR][1000 genomes]
rs12291620	1.00[JPT][hapmap]
rs12419511	0.85[JPT][hapmap]
rs12422179	1.00[JPT][hapmap]
rs12790943	0.92[EUR][1000 genomes]
rs12791292	0.92[EUR][1000 genomes]
rs2444239	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3740728	0.85[JPT][hapmap]
rs3740729	0.85[JPT][hapmap]
rs3740731	0.85[JPT][hapmap]
rs508205	0.89[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7116997	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7118957	1.00[JPT][hapmap]
rs7119458	1.00[JPT][hapmap]
rs880487	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs896693	CD3D	cis	cerebellum	SCAN
rs896693	TMPRSS13	cis	cerebellum	SCAN
rs896693	DPAGT1	cis	cerebellum	SCAN
rs896693	FXYD6	cis	cerebellum	SCAN
rs896693	CCDC84	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120058000-120068800	Weak transcription	Right Atrium	heart
2	chr11:120058200-120068200	Weak transcription	Spleen	Spleen
3	chr11:120059400-120067200	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:120060000-120067400	Weak transcription	Right Ventricle	heart
5	chr11:120062200-120073600	Enhancers	Fetal Intestine Small	intestine
6	chr11:120064200-120070400	Enhancers	Fetal Muscle Leg	muscle
7	chr11:120064400-120067200	Weak transcription	Small Intestine	intestine
8	chr11:120064400-120070200	Enhancers	Fetal Muscle Trunk	muscle
9	chr11:120064600-120067400	Enhancers	HepG2	liver
10	chr11:120064600-120069200	Weak transcription	Ovary	ovary
11	chr11:120064600-120069400	Weak transcription	Pancreas	Pancrea
12	chr11:120065600-120071800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr11:120065800-120068200	Enhancers	Colonic Mucosa	Colon
14	chr11:120065800-120068200	Enhancers	Fetal Kidney	kidney
15	chr11:120065800-120068800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr11:120065800-120069400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:120065800-120070400	Enhancers	Fetal Stomach	stomach
18	chr11:120065800-120074600	Enhancers	Fetal Intestine Large	intestine
19	chr11:120066000-120067600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:120066000-120068600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr11:120066000-120069200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:120066000-120069800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:120066200-120067400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:120066200-120068000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:120066400-120067200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr11:120066400-120067400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:120066400-120068600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:120066400-120068600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr11:120066400-120069200	Enhancers	Placenta	Placenta
30	chr11:120066400-120069600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:120066400-120069800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:120066400-120069800	Enhancers	Fetal Lung	lung
33	chr11:120066400-120070200	Enhancers	Brain Cingulate Gyrus	brain
34	chr11:120066400-120070200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr11:120066400-120070800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr11:120066400-120071000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr11:120066600-120067600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr11:120066600-120069800	Enhancers	Brain Hippocampus Middle	brain
39	chr11:120066600-120073200	Enhancers	Duodenum Mucosa	Duodenum
40	chr11:120066800-120068000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
41	chr11:120066800-120069800	Enhancers	Brain Anterior Caudate	brain
42	chr11:120066800-120070400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr11:120066800-120070800	Enhancers	Liver	Liver
44	chr11:120066800-120071200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
45	chr11:120066800-120071200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
46	chr11:120067000-120067200	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr11:120067000-120067600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr11:120067000-120069200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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