Variant report

Variant	rs11704358
Chromosome Location	chr22:30672352-30672353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30660224..30662293-chr22:30672122..30673806,2	K562	blood:
2	chr22:30668087..30672476-chr22:30679635..30681942,4	K562	blood:
3	chr22:30671566..30674215-chr22:30702631..30704760,2	MCF-7	breast:
4	chr22:30671223..30673243-chr22:30676654..30678406,2	MCF-7	breast:
5	chr22:30669173..30672631-chr22:30679828..30683930,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GATSL3-2	chr22:30671204-30672940	NONHSAT084762

No data

Variant related genes	Relation type
ENSG00000099992	Chromatin interaction
ENSG00000099985	Chromatin interaction
ENSG00000239282	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11089441	1.00[LWK][hapmap];0.85[MKK][hapmap]
rs11089442	1.00[LWK][hapmap]
rs12484252	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2839998	1.00[LWK][hapmap]
rs8141656	1.00[LWK][hapmap]
rs929271	1.00[LWK][hapmap]
rs9619096	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11704358	THOC5	cis	parietal	SCAN
rs11704358	TCN2	cis	lymphoblastoid	seeQTL
rs11704358	RNF185	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30659600-30673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr22:30662800-30673400	Weak transcription	Right Atrium	heart
3	chr22:30663600-30673800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:30663800-30674000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr22:30664000-30673000	Weak transcription	Colonic Mucosa	Colon
6	chr22:30668000-30673600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr22:30669400-30672400	Enhancers	Placenta	Placenta
8	chr22:30669400-30676800	Enhancers	Adipose Nuclei	Adipose
9	chr22:30670000-30673200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr22:30670200-30673000	Weak transcription	Osteobl	bone
11	chr22:30670200-30673400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:30670200-30673600	Weak transcription	Brain Substantia Nigra	brain
13	chr22:30670200-30673800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:30670400-30673000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr22:30670400-30673000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr22:30670400-30673800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr22:30670400-30673800	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:30670400-30673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr22:30670400-30674400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr22:30670600-30674000	Weak transcription	Brain Anterior Caudate	brain
21	chr22:30671000-30672600	Flanking Active TSS	Dnd41	blood
22	chr22:30671000-30673800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr22:30671000-30674200	Weak transcription	Lung	lung
24	chr22:30671200-30672600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr22:30671200-30672600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:30671200-30672800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
27	chr22:30671400-30672400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr22:30671400-30672400	Enhancers	Stomach Mucosa	stomach
29	chr22:30671400-30672600	Enhancers	Fetal Thymus	thymus
30	chr22:30671400-30672600	Enhancers	Thymus	Thymus
31	chr22:30671400-30672800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:30671400-30674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr22:30671600-30672400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr22:30671600-30672400	Enhancers	Spleen	Spleen
35	chr22:30671600-30672600	Enhancers	Primary T cells from cord blood	blood
36	chr22:30671600-30672600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr22:30671600-30673200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr22:30671600-30674000	Enhancers	Duodenum Mucosa	Duodenum
39	chr22:30671600-30674600	Enhancers	Primary hematopoietic stem cells	blood
40	chr22:30671600-30675600	Enhancers	Fetal Intestine Small	intestine
41	chr22:30671800-30672400	Enhancers	Primary B cells from cord blood	blood
42	chr22:30671800-30672400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr22:30671800-30672400	Enhancers	K562	blood
44	chr22:30671800-30672600	Enhancers	Primary B cells from peripheral blood	blood
45	chr22:30671800-30674400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr22:30672000-30673000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr22:30672000-30673000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr22:30672000-30674000	Weak transcription	Esophagus	oesophagus
49	chr22:30672200-30672400	Enhancers	GM12878-XiMat	blood
50	chr22:30672200-30672600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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