Variant report

Variant	rs60255904
Chromosome Location	chr1:227975414-227975415
allele	A/C
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:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227966135..227968360-chr1:227973552..227975937,2	MCF-7	breast:
2	chr1:227973990..227976500-chr1:228134426..228136462,3	MCF-7	breast:
3	chr1:227967943..227969824-chr1:227975075..227977321,2	K562	blood:
4	chr1:227973508..227976414-chr1:228271906..228274660,2	K562	blood:
5	chr1:227945394..227947244-chr1:227973849..227976801,2	MCF-7	breast:
6	chr1:227962656..227964965-chr1:227972636..227975785,3	MCF-7	breast:
7	chr1:227970937..227973164-chr1:227974338..227975949,2	K562	blood:
8	chr1:227960240..227967392-chr1:227972741..227977657,8	K562	blood:
9	chr1:227921116..227924283-chr1:227974450..227977412,3	MCF-7	breast:
10	chr1:227974881..227977726-chr20:49346280..49347834,2	MCF-7	breast:
11	chr1:227973847..227976813-chr1:228134403..228136465,4	MCF-7	breast:
12	chr1:227974795..227976825-chr1:227979678..227981441,2	MCF-7	breast:
13	chr1:227970651..227973164-chr1:227973342..227975838,2	K562	blood:
14	chr1:227974971..227975949-chr1:228089646..228090423,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAP47-1	chr1:227975396-227975712	NONHSAT009948

No data

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12566948	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60156730	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6684706	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7543525	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
12	esv3441420	chr1:227974754-227977302	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv3380731	chr1:227975029-227977177	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60255904	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227973600-227975800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr1:227973600-227975800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr1:227974400-227975600	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr1:227974400-227975600	Flanking Bivalent TSS/Enh	HepG2	liver
5	chr1:227974600-227975600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:227974600-227975600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:227974600-227975600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
8	chr1:227974600-227975800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:227974600-227977000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:227974800-227975600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:227974800-227975600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr1:227974800-227975600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:227974800-227975600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:227974800-227975600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:227974800-227975600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:227974800-227975600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr1:227974800-227975600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
18	chr1:227974800-227975600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:227974800-227975600	Flanking Active TSS	HMEC	breast
20	chr1:227974800-227975600	Flanking Active TSS	HSMMtube	muscle
21	chr1:227974800-227975800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:227974800-227975800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
24	chr1:227974800-227975800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:227974800-227975800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:227974800-227975800	Flanking Active TSS	Liver	Liver
29	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr1:227974800-227975800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
33	chr1:227974800-227975800	Flanking Active TSS	HSMM	muscle
34	chr1:227974800-227976800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr1:227974800-227977000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr1:227974800-227977200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:227974800-227977200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr1:227974800-227977400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:227975000-227975600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:227975000-227975600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
41	chr1:227975000-227975600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr1:227975000-227975600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr1:227975000-227975600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:227975000-227975600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:227975000-227975600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:227975000-227975600	Flanking Active TSS	Colonic Mucosa	Colon
47	chr1:227975000-227975600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
48	chr1:227975000-227975600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr1:227975000-227975600	Flanking Active TSS	Stomach Mucosa	stomach
50	chr1:227975000-227975600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel

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