Variant report

Variant	rs11616606
Chromosome Location	chr13:52344394-52344395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52024516..52028939-chr13:52342727..52345568,4	MCF-7	breast:
2	chr13:52025577..52029967-chr13:52343918..52348772,7	MCF-7	breast:
3	chr13:52025721..52028178-chr13:52344318..52347110,2	K562	blood:
4	chr13:52024690..52027265-chr13:52341888..52344446,2	K562	blood:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10676	1.00[CHD][hapmap]
rs11148228	1.00[CHD][hapmap]
rs11616240	0.92[EUR][1000 genomes]
rs11618231	0.92[EUR][1000 genomes]
rs17597763	0.95[EUR][1000 genomes]
rs4113264	1.00[CHD][hapmap]
rs9596560	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised 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	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11616606	TMEM22	trans	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52330600-52355600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:52335200-52347000	Weak transcription	Fetal Brain Male	brain
3	chr13:52335200-52348000	Weak transcription	Fetal Brain Female	brain
4	chr13:52339400-52345000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr13:52339400-52347000	Weak transcription	A549	lung
6	chr13:52339400-52347600	Weak transcription	Aorta	Aorta
7	chr13:52339400-52347600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:52339400-52347800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:52339400-52349600	Weak transcription	Placenta	Placenta
10	chr13:52339400-52352000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr13:52339400-52356200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:52339400-52357400	Weak transcription	Colonic Mucosa	Colon
13	chr13:52339600-52344400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:52339600-52356800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:52339600-52361400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:52339800-52345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:52339800-52345600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:52339800-52346200	Strong transcription	Primary T cells from cord blood	blood
20	chr13:52339800-52359800	Weak transcription	Colon Smooth Muscle	Colon
21	chr13:52339800-52371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr13:52339800-52375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:52340400-52346400	Strong transcription	Thymus	Thymus
24	chr13:52340400-52348200	Strong transcription	Fetal Stomach	stomach
25	chr13:52340800-52352200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr13:52341200-52347800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:52341400-52354600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:52341400-52361200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr13:52341600-52345000	Weak transcription	NHLF	lung
30	chr13:52341600-52352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:52341600-52356400	Weak transcription	Brain Germinal Matrix	brain
32	chr13:52341800-52346800	Weak transcription	Osteobl	bone
33	chr13:52342200-52346400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr13:52342400-52344400	Enhancers	Fetal Muscle Trunk	muscle
35	chr13:52342400-52344600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:52342400-52344600	Genic enhancers	Lung	lung
37	chr13:52342400-52344600	Enhancers	Spleen	Spleen
38	chr13:52342400-52344800	Enhancers	Right Ventricle	heart
39	chr13:52342400-52344800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr13:52342400-52346200	Enhancers	Left Ventricle	heart
41	chr13:52342400-52347800	Enhancers	Right Atrium	heart
42	chr13:52342400-52348200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:52342600-52345400	Weak transcription	NHEK	skin
44	chr13:52342600-52356200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:52342800-52345600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr13:52342800-52355800	Weak transcription	Primary B cells from cord blood	blood
47	chr13:52343000-52345200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:52343000-52351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:52343200-52344600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr13:52343200-52345000	Enhancers	Adipose Nuclei	Adipose

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