Variant report

Variant	rs41314549
Chromosome Location	chr1:155290231-155290232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155289700-155291469	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:155290203-155290900	K562	blood:	n/a	n/a
3	POLR2A	chr1:155289045-155291721	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:155289890-155290299	MCF10A-Er-Src	breast:	n/a	n/a
5	REST	chr1:155290193-155291335	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr1:155289697-155291331	K562	blood:	n/a	n/a
7	POLR2A	chr1:155289217-155291291	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:155285762-155295040	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:155289618-155291946	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr1:155289966-155291313	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:155288287-155291476	U87	brain:	n/a	n/a
12	SP1	chr1:155290104-155290705	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:155285992-155291727	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:155287588-155292287	HL-60	blood:	n/a	n/a
15	POLR2A	chr1:155287550-155292168	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:155286497-155292073	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr1:155289598-155291380	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:155287495-155292212	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:155287514-155291951	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:155289543-155291208	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:155289357-155291175	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:155290040-155290985	HEK293	kidney:	n/a	n/a
23	POLR2A	chr1:155290126-155291646	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:155289636-155290400	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:155285720-155292259	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr1:155287685-155291891	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:155289663-155291669	U87	brain:	n/a	n/a
28	POLR2A	chr1:155289172-155292119	K562	blood:	n/a	n/a
29	POLR2A	chr1:155289709-155291109	K562	blood:	n/a	n/a
30	POLR2A	chr1:155288607-155291751	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:155289133-155292282	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr1:155290057-155290257	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr1:155290150-155290468	T-47D	breast:	n/a	n/a
34	NRF1	chr1:155290170-155291419	SK-N-SH	brain:	n/a	chr1:155290659-155290670 chr1:155290641-155290652
35	POLR2A	chr1:155288293-155291535	U87	brain:	n/a	n/a
36	POLR2A	chr1:155288780-155290947	PBDE	blood:	n/a	n/a
37	POLR2A	chr1:155286517-155292132	K562	blood:	n/a	n/a
38	POLR2A	chr1:155288646-155291237	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr1:155286610-155292157	K562	blood:	n/a	n/a
40	POLR2A	chr1:155289783-155291567	K562	blood:	n/a	n/a
41	POLR2A	chr1:155287248-155291990	PFSK-1	brain:	n/a	n/a
42	CTCF	chr1:155290220-155290370	HUVEC	blood vessel:	n/a	n/a
43	SIN3AK20	chr1:155290022-155291163	PANC-1	pancreas:	n/a	n/a
44	MXI1	chr1:155289939-155295400	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr1:155289656-155291669	U87	brain:	n/a	n/a
46	POLR2A	chr1:155289809-155291005	K562	blood:	n/a	n/a
47	POLR2A	chr1:155288984-155291335	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr1:155289042-155291565	K562	blood:	n/a	n/a
49	POLR2A	chr1:155286649-155291520	GM12891	blood:	n/a	n/a
50	POLR2A	chr1:155289717-155291560	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155175235..155178055-chr1:155287836..155290793,2	MCF-7	breast:
2	chr1:155245096..155252304-chr1:155290044..155297941,20	MCF-7	breast:
3	chr1:155226986..155228712-chr1:155289329..155291450,2	K562	blood:
4	chr1:155213696..155217007-chr1:155289069..155291862,3	K562	blood:
5	chr1:155240682..155244991-chr1:155289682..155296120,12	MCF-7	breast:
6	chr1:155218456..155235751-chr1:155288837..155299195,44	MCF-7	breast:
7	chr1:155239314..155245036-chr1:155288379..155297041,21	MCF-7	breast:
8	chr1:155231157..155233872-chr1:155289047..155290722,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASH1L-1	chr1:155289950-155291486	ENSG00000225855.2

No data

Variant related genes	Relation type
RUSC1	TF binding region
ENSG00000160767	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000143630	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000177628	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs72704130	1.00[AMR][1000 genomes]
rs72704164	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72704191	1.00[AMR][1000 genomes]
rs72704192	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
2	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
3	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	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
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	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
8	nsv946413	chr1:155286949-155296660	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41314549	RIT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155279200-155290400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155279800-155290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155280000-155290400	Weak transcription	Psoas Muscle	Psoas
4	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:155280800-155290600	Weak transcription	Small Intestine	intestine
7	chr1:155281400-155290600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:155281600-155290600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:155282200-155290600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:155283600-155290400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:155286200-155290800	Strong transcription	Dnd41	blood
12	chr1:155286600-155290400	Genic enhancers	K562	blood
13	chr1:155286600-155290600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:155286600-155290600	Strong transcription	Hela-S3	cervix
15	chr1:155287000-155290400	Strong transcription	Liver	Liver
16	chr1:155287200-155290600	Strong transcription	A549	lung
17	chr1:155287200-155290600	Strong transcription	HepG2	liver
18	chr1:155287600-155290800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:155287800-155293200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:155288200-155290400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:155288600-155290400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:155288800-155290400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:155288800-155290600	Genic enhancers	HMEC	breast
24	chr1:155289000-155290400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:155289000-155290400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:155289200-155292000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:155289600-155290400	Weak transcription	HSMM	muscle
28	chr1:155289800-155290400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:155289800-155290400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:155289800-155290400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:155289800-155290400	Enhancers	Fetal Heart	heart
32	chr1:155289800-155290400	Weak transcription	Lung	lung
33	chr1:155289800-155290400	Enhancers	Spleen	Spleen
34	chr1:155289800-155290600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:155289800-155291000	Flanking Active TSS	Fetal Lung	lung
36	chr1:155289800-155291400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:155289800-155292000	Transcr. at gene 5' and 3'	NHLF	lung
38	chr1:155290000-155290400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:155290000-155290400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:155290000-155290400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:155290000-155290400	Enhancers	Primary B cells from peripheral blood	blood
42	chr1:155290000-155290400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:155290000-155290400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr1:155290000-155290400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:155290000-155290400	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr1:155290000-155290400	Enhancers	Esophagus	oesophagus
47	chr1:155290000-155290400	Enhancers	Placenta	Placenta
48	chr1:155290000-155290400	Weak transcription	Gastric	stomach
49	chr1:155290000-155290400	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr1:155290000-155290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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