Variant report

Variant	rs4754715
Chromosome Location	chr11:100851247-100851248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:100850328..100852542-chr11:100997954..101000067,2	MCF-7	breast:
2	chr11:100851180..100854144-chr11:100858258..100861196,2	K562	blood:
3	chr11:100850533..100851521-chr11:100874106..100874843,2	MCF-7	breast:
4	chr11:100851062..100853644-chr11:100861748..100863758,2	MCF-7	breast:
5	chr11:100851058..100853981-chr11:101168719..101170775,2	MCF-7	breast:
6	chr11:100849467..100854913-chr11:100993227..101000778,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170647	Chromatin interaction
ENSG00000082175	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10488785	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2509107	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs471933	0.87[CEU][hapmap]
rs4754707	0.80[EUR][1000 genomes]
rs483657	0.84[AFR][1000 genomes]
rs524811	1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.93[AFR][1000 genomes]
rs535747	0.85[CEU][hapmap]
rs561268	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs581921	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs612046	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs629813	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs634636	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs651301	0.94[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs664212	0.92[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048356	chr11:100713096-101058995	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv541154	chr11:100713096-101058995	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4754715	MARK1	trans	parietal	SCAN
rs4754715	TMEM133	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100810000-100852200	Weak transcription	Small Intestine	intestine
2	chr11:100830600-100858200	Weak transcription	Colonic Mucosa	Colon
3	chr11:100834400-100851600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:100841600-100852200	Weak transcription	Spleen	Spleen
5	chr11:100841800-100852200	Weak transcription	Esophagus	oesophagus
6	chr11:100844000-100860200	Strong transcription	Placenta	Placenta
7	chr11:100844800-100863000	Weak transcription	Brain Anterior Caudate	brain
8	chr11:100846200-100857400	Weak transcription	Fetal Brain Male	brain
9	chr11:100846400-100855200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:100847000-100855200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:100847800-100852200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:100847800-100854400	Weak transcription	Right Ventricle	heart
13	chr11:100848000-100851800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:100848000-100861800	Weak transcription	Fetal Heart	heart
15	chr11:100848200-100851600	Weak transcription	Ovary	ovary
16	chr11:100848200-100856200	Weak transcription	Fetal Intestine Small	intestine
17	chr11:100848200-100856400	Weak transcription	Fetal Stomach	stomach
18	chr11:100848200-100857400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:100848200-100858600	Weak transcription	Gastric	stomach
20	chr11:100848200-100859600	Weak transcription	Stomach Mucosa	stomach
21	chr11:100848200-100861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:100848200-100866000	Weak transcription	Psoas Muscle	Psoas
23	chr11:100848400-100851800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:100848400-100852400	Weak transcription	Primary T cells from cord blood	blood
25	chr11:100848400-100859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:100848400-100859800	Weak transcription	Fetal Kidney	kidney
27	chr11:100848400-100860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:100848400-100863200	Weak transcription	Fetal Intestine Large	intestine
29	chr11:100848400-100864600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:100848600-100852800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:100848600-100859200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:100848600-100863400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:100848600-100865200	Weak transcription	Left Ventricle	heart
34	chr11:100848600-100865800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:100848800-100855000	Weak transcription	Primary B cells from cord blood	blood
36	chr11:100848800-100857600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:100848800-100858000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:100848800-100860000	Weak transcription	NH-A	brain
39	chr11:100848800-100864800	Weak transcription	HSMM	muscle
40	chr11:100849000-100852200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:100849000-100862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:100849000-100863000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:100849200-100867400	Weak transcription	Fetal Lung	lung
44	chr11:100849600-100856200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:100849800-100856400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:100850000-100852200	Weak transcription	HSMMtube	muscle
47	chr11:100850000-100859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:100850000-100861600	Weak transcription	Adipose Nuclei	Adipose
49	chr11:100850400-100852200	Weak transcription	Liver	Liver
50	chr11:100850600-100864600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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