Variant report

Variant	rs2172700
Chromosome Location	chr1:220924629-220924630
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr1:220924572-220924766	HepG2	liver:	n/a	chr1:220924641-220924656 chr1:220924586-220924598 chr1:220924640-220924655 chr1:220924641-220924656 chr1:220924647-220924655 chr1:220924641-220924656 chr1:220924641-220924656

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220922191..220924696-chr1:220926273..220928216,2	MCF-7	breast:
2	chr1:220923442..220925865-chr7:104652802..104654696,2	MCF-7	breast:

Variant related genes	Relation type
MARC2	TF binding region
ENSG00000005483	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000239569	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17008595	0.82[ASN][1000 genomes]
rs17008643	0.80[ASN][1000 genomes]
rs2088044	0.85[EUR][1000 genomes]
rs2101771	0.85[EUR][1000 genomes]
rs2172699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279636	0.80[ASN][1000 genomes]
rs2279637	0.80[ASN][1000 genomes]
rs58055537	0.81[EUR][1000 genomes]
rs6673650	0.81[EUR][1000 genomes]
rs72472365	0.87[EUR][1000 genomes]
rs72472382	0.92[ASN][1000 genomes]

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	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2172700	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs2172700	MOSC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220921400-220924800	Active TSS	Fetal Intestine Small	intestine
2	chr1:220922400-220932200	Weak transcription	HSMMtube	muscle
3	chr1:220922600-220925200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:220922600-220925200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:220922600-220925400	Weak transcription	Gastric	stomach
6	chr1:220922600-220927000	Weak transcription	Small Intestine	intestine
7	chr1:220922600-220928800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:220922600-220929400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:220922600-220929400	Weak transcription	Esophagus	oesophagus
10	chr1:220922600-220931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:220922800-220924800	Enhancers	Fetal Stomach	stomach
14	chr1:220922800-220925200	Enhancers	Stomach Mucosa	stomach
15	chr1:220922800-220925400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:220922800-220926000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:220922800-220929000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:220923000-220924800	Flanking Active TSS	Fetal Lung	lung
21	chr1:220923000-220925200	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr1:220923200-220925200	Enhancers	Colonic Mucosa	Colon
23	chr1:220923200-220925600	Enhancers	HepG2	liver
24	chr1:220923200-220926600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:220923200-220927200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:220923200-220927400	Enhancers	Pancreas	Pancrea
27	chr1:220923200-220930400	Weak transcription	Spleen	Spleen
28	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:220923400-220925000	Weak transcription	Lung	lung
30	chr1:220923400-220927000	Enhancers	Right Ventricle	heart
31	chr1:220923600-220925000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
32	chr1:220923600-220925000	Enhancers	Brain Germinal Matrix	brain
33	chr1:220923600-220926200	Enhancers	Psoas Muscle	Psoas
34	chr1:220923800-220925000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr1:220923800-220925000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr1:220923800-220925200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:220923800-220925200	Enhancers	Colon Smooth Muscle	Colon
38	chr1:220923800-220925600	Enhancers	Fetal Muscle Leg	muscle
39	chr1:220923800-220925800	Enhancers	Ovary	ovary
40	chr1:220923800-220928200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:220923800-220928200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:220923800-220928200	Weak transcription	Placenta	Placenta
43	chr1:220923800-220928400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:220924000-220924800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr1:220924000-220924800	Enhancers	Brain Anterior Caudate	brain
46	chr1:220924000-220924800	Active TSS	Duodenum Mucosa	Duodenum
47	chr1:220924000-220925000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr1:220924000-220925200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:220924000-220925200	Enhancers	Brain Cingulate Gyrus	brain
50	chr1:220924000-220925200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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