Variant report

Variant	rs4661218
Chromosome Location	chr1:155960185-155960186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:155959587-155960341	GM12878	blood:	n/a	n/a
2	MYC	chr1:155959813-155960188	NB4	blood:	n/a	n/a
3	POLR2A	chr1:155959728-155960518	HL-60	blood:	n/a	n/a
4	SPI1	chr1:155959473-155960219	GM12878	blood:	n/a	chr1:155959953-155959966 chr1:155959914-155959921
5	MTA3	chr1:155958918-155960304	GM12878	blood:	n/a	n/a
6	EGR1	chr1:155960156-155960434	K562	blood:	n/a	n/a
7	POLR2A	chr1:155959745-155960461	HL-60	blood:	n/a	n/a
8	MAX	chr1:155959772-155960197	NB4	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155958637..155961186-chr1:155975621..155978419,3	MCF-7	breast:
2	chr1:155959707..155961223-chr1:156023678..156026675,2	K562	blood:
3	chr1:155902871..155906324-chr1:155958036..155960843,4	K562	blood:
4	chr1:155903740..155906324-chr1:155958823..155960843,2	K562	blood:
5	chr1:155946653..155948454-chr1:155959056..155961851,2	K562	blood:
6	chr1:155902685..155905586-chr1:155957752..155961229,4	MCF-7	breast:
7	chr1:155935970..155939693-chr1:155959127..155962229,3	K562	blood:

No data

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000224276	TF binding region
ENSG00000132680	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000116586	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10796955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1111102	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs11264422	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11264426	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11585845	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12118795	0.90[CEU][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap]
rs12568523	0.95[CEU][hapmap]
rs1749405	0.80[CHB][hapmap]
rs1889532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889533	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs2282301	0.95[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2297649	0.95[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2364403	0.82[MEX][hapmap]
rs2993207	0.80[CHB][hapmap]
rs3856261	0.88[JPT][hapmap]
rs4661175	0.86[ASW][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4661217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488079	0.80[CHB][hapmap]
rs490498	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs539602	0.80[CHB][hapmap]
rs61813286	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625658	0.80[CHB][hapmap]
rs6427297	0.81[CEU][hapmap]
rs6667652	0.95[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs6670493	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696019	0.95[CEU][hapmap]
rs670523	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs729022	0.82[MEX][hapmap]
rs7534858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs822478	0.89[JPT][hapmap]
rs867549	0.95[CEU][hapmap];0.91[MEX][hapmap]
rs867550	0.95[CEU][hapmap];0.91[MEX][hapmap]
rs915178	0.86[CEU][hapmap]
rs915181	0.95[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs928596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4661218	ROBLD3	cis	parietal	SCAN
rs4661218	YY1AP1	cis	cerebellum	SCAN
rs4661218	PRUNE	cis	cerebellum	SCAN
rs4661218	RIT1	cis	Thyroid	GTEx
rs4661218	SPRR3	cis	parietal	SCAN
rs4661218	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs4661218	RIT1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155952000-155960800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:155953600-155960800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:155954400-155960800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155954600-155970800	Weak transcription	NHEK	skin
5	chr1:155958600-155960600	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:155958600-155961000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:155958600-155961600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:155958800-155960600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:155958800-155961600	Enhancers	Placenta	Placenta
10	chr1:155959000-155960400	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:155959000-155960800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:155959000-155961800	Enhancers	Liver	Liver
13	chr1:155959200-155961000	Weak transcription	NH-A	brain
14	chr1:155959200-155966000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:155959200-155978200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:155959400-155960200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr1:155959400-155960400	Enhancers	Fetal Kidney	kidney
18	chr1:155959400-155960600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:155959400-155960600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:155959400-155960600	Weak transcription	Fetal Brain Female	brain
21	chr1:155959400-155960800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:155959400-155960800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:155959400-155960800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:155959400-155960800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:155959400-155960800	Enhancers	Fetal Muscle Leg	muscle
26	chr1:155959400-155960800	Enhancers	Spleen	Spleen
27	chr1:155959400-155960800	Weak transcription	HMEC	breast
28	chr1:155959400-155961600	Enhancers	NHDF-Ad	bronchial
29	chr1:155959400-155962000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:155959400-155965000	Weak transcription	Pancreas	Pancrea
31	chr1:155959400-155965800	Weak transcription	HSMMtube	muscle
32	chr1:155959400-155970800	Weak transcription	Colonic Mucosa	Colon
33	chr1:155959400-155976600	Weak transcription	Aorta	Aorta
34	chr1:155959600-155960200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:155959600-155960400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:155959600-155960600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:155959600-155960600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:155959600-155960600	Weak transcription	Lung	lung
39	chr1:155959600-155960600	Genic enhancers	Hela-S3	cervix
40	chr1:155959600-155960800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:155959600-155960800	Weak transcription	HSMM	muscle
42	chr1:155959600-155960800	Weak transcription	NHLF	lung
43	chr1:155959600-155960800	Weak transcription	Osteobl	bone
44	chr1:155959600-155961200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:155959600-155964400	Weak transcription	Fetal Intestine Large	intestine
46	chr1:155959600-155964400	Weak transcription	Fetal Intestine Small	intestine
47	chr1:155959600-155965400	Weak transcription	Right Atrium	heart
48	chr1:155959600-155970400	Weak transcription	Stomach Mucosa	stomach
49	chr1:155959600-155971000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:155959600-155971800	Weak transcription	Gastric	stomach

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