Variant report

Variant	rs348192
Chromosome Location	chr1:155668062-155668063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155656893..155661917-chr1:155662515..155668604,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132676	Chromatin interaction
ENSG00000163374	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10908479	0.84[AMR][1000 genomes]
rs12035524	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12744132	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2175391	0.82[AMR][1000 genomes]
rs348186	0.84[AMR][1000 genomes]
rs348196	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs475550	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4971095	0.80[AMR][1000 genomes]
rs6672128	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs670876	0.85[AMR][1000 genomes]
rs678157	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7521594	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	nsv3054	chr1:155653835-155673509	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
12	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs348192	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155659400-155668200	Weak transcription	Aorta	Aorta
2	chr1:155660200-155698800	Weak transcription	NHLF	lung
3	chr1:155660400-155668400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:155660400-155671000	Weak transcription	Esophagus	oesophagus
5	chr1:155660400-155675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:155660400-155682800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:155660400-155688800	Weak transcription	Lung	lung
8	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
9	chr1:155660600-155679000	Weak transcription	Fetal Brain Female	brain
10	chr1:155660600-155680200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:155660800-155682600	Weak transcription	Spleen	Spleen
12	chr1:155661600-155688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
14	chr1:155661800-155668400	Weak transcription	NH-A	brain
15	chr1:155662200-155669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:155662200-155682000	Weak transcription	HSMMtube	muscle
17	chr1:155662400-155668400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:155662400-155682800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:155662400-155685600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:155662600-155669200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:155662600-155673800	Weak transcription	HMEC	breast
22	chr1:155662800-155668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:155663000-155679400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:155663000-155681200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:155663200-155668200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:155663200-155668200	Weak transcription	Osteobl	bone
27	chr1:155663200-155668600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:155663200-155675800	Weak transcription	HSMM	muscle
29	chr1:155663200-155679200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:155663200-155701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:155663400-155682600	Weak transcription	Primary B cells from cord blood	blood
32	chr1:155664400-155674600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:155664400-155678800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:155664400-155679000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:155665000-155673600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:155665000-155678600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:155665200-155668400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:155665200-155668600	Weak transcription	Fetal Heart	heart
39	chr1:155665200-155673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:155665200-155676000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:155665200-155685800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:155665200-155708000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:155665400-155668200	Weak transcription	Gastric	stomach
44	chr1:155665400-155668200	Enhancers	HepG2	liver
45	chr1:155665400-155668400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:155665400-155669400	Weak transcription	Fetal Thymus	thymus
47	chr1:155665400-155673200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:155665400-155675800	Weak transcription	NHDF-Ad	bronchial
49	chr1:155665400-155678800	Weak transcription	Thymus	Thymus
50	chr1:155665400-155678800	Weak transcription	Dnd41	blood

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