Variant report

Variant	rs4754702
Chromosome Location	chr11:100696230-100696231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:100691211..100693446-chr11:100695155..100697505,2	K562	blood:
2	chr11:100687804..100689545-chr11:100695788..100697568,2	K562	blood:
3	chr11:100694680..100697699-chr17:41464181..41467943,10	K562	blood:
4	chr11:100696179..100697700-chr17:41399375..41402173,3	K562	blood:
5	chr11:100696199..100697700-chr17:41464901..41467783,3	K562	blood:
6	chr11:100694700..100697700-chr17:41439505..41443891,3	K562	blood:

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10894999	1.00[JPT][hapmap]
rs10895000	1.00[JPT][hapmap]
rs17095426	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]
rs17095428	1.00[CHB][hapmap]
rs17095429	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]
rs17095438	1.00[CHB][hapmap]
rs17095439	1.00[CHB][hapmap]
rs17573475	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4121392	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs499241	0.81[ASW][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap]
rs507695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs58626072	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61890781	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61890787	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682847	0.92[ASN][1000 genomes]
rs7105842	1.00[CHB][hapmap]
rs7110872	1.00[CHB][hapmap]
rs7120712	1.00[CHB][hapmap]
rs7927197	1.00[CHB][hapmap]
rs7942588	1.00[CHB][hapmap]
rs7947761	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4754702	TMEM133	cis	cerebellum	SCAN
rs4754702	MMP20	cis	cerebellum	SCAN
rs4754702	ARHGAP42	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100670000-100697400	Weak transcription	Placenta	Placenta
2	chr11:100680800-100696400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:100681200-100698000	Weak transcription	Stomach Mucosa	stomach
4	chr11:100681400-100701000	Weak transcription	HSMM	muscle
5	chr11:100686200-100702800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:100688000-100698600	Weak transcription	NH-A	brain
7	chr11:100688000-100704000	Weak transcription	Right Ventricle	heart
8	chr11:100689000-100698600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:100689200-100698200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:100690400-100696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:100690800-100697200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr11:100691800-100696800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr11:100691800-100696800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:100692200-100698000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:100692800-100696400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:100692800-100698200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:100693600-100697000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr11:100693600-100697000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr11:100693600-100697200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr11:100693600-100697200	Enhancers	Fetal Kidney	kidney
21	chr11:100694200-100696400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:100694200-100696400	Weak transcription	Brain Anterior Caudate	brain
23	chr11:100694200-100696400	Weak transcription	Brain Germinal Matrix	brain
24	chr11:100694200-100698000	Weak transcription	Fetal Heart	heart
25	chr11:100694200-100698000	Weak transcription	Left Ventricle	heart
26	chr11:100694200-100698200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:100694200-100698400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:100694400-100696400	Weak transcription	Small Intestine	intestine
29	chr11:100694400-100701000	Weak transcription	HSMMtube	muscle
30	chr11:100694600-100698600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:100694800-100698200	Weak transcription	NHLF	lung
32	chr11:100695000-100696400	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:100695000-100697200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr11:100695000-100697800	Weak transcription	Right Atrium	heart
35	chr11:100695000-100701000	Weak transcription	Psoas Muscle	Psoas
36	chr11:100695200-100696400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:100695200-100698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:100695200-100698600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr11:100695400-100696600	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:100695400-100698000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:100695400-100698000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:100695600-100697800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:100695600-100698000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:100695600-100698000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:100695600-100698600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:100695800-100698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:100696000-100696400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:100696000-100696600	Enhancers	A549	lung
49	chr11:100696000-100696800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:100696000-100696800	Enhancers	Adipose Nuclei	Adipose

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