Variant report

Variant	rs10908486
Chromosome Location	chr1:155978544-155978545
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155978475-155978903	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:155978327-155978890	GM12878	blood:	n/a	n/a
3	CTCF	chr1:155978420-155978570	GM12864	blood:	n/a	n/a
4	CTCF	chr1:155978400-155978550	AG10803	skin:	n/a	n/a
5	GATA3	chr1:155978260-155978654	T-47D	breast:	n/a	n/a
6	MAFF	chr1:155978487-155979048	K562	blood:	n/a	chr1:155978869-155978887
7	CTCF	chr1:155978440-155978590	HA-sp	spinal cord:	n/a	n/a
8	CTCF	chr1:155978500-155978650	WI-38	lung:	n/a	n/a
9	POLR2A	chr1:155978164-155978889	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:155978174-155979633	PFSK-1	brain:	n/a	n/a
11	CTCF	chr1:155978400-155978550	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr1:155978540-155978690	HPF	lung:	n/a	n/a
13	CTCF	chr1:155978400-155978550	HRPEpiC	eye:	n/a	n/a
14	POLR2A	chr1:155978276-155978930	K562	blood:	n/a	n/a
15	POLR2A	chr1:155978353-155978865	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:155978538-155978827	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:155978418-155978745	K562	blood:	n/a	n/a
18	MAFK	chr1:155978490-155979070	Hela-S3	cervix:	n/a	chr1:155978870-155978885 chr1:155978506-155978516
19	POLR2A	chr1:155978518-155978754	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:155978238-155978764	SK-N-SH	brain:	n/a	n/a
21	GATA3	chr1:155978141-155978889	MCF-7	breast:	n/a	chr1:155978825-155978836
22	CTCF	chr1:155978520-155978670	GM12872	blood:	n/a	n/a
23	CTCF	chr1:155978314-155978619	MCF-7	breast:	n/a	n/a
24	CTCF	chr1:155978420-155978570	GM12868	blood:	n/a	n/a
25	RAD21	chr1:155978369-155978589	Hela-S3	cervix:	n/a	n/a
26	ZNF384	chr1:155978275-155978698	K562	blood:	n/a	n/a
27	POLR2A	chr1:155978441-155978877	GM12892	blood:	n/a	n/a
28	CTCF	chr1:155978420-155978570	HMF	breast:	n/a	n/a
29	CTCF	chr1:155978400-155978550	SAEC	small airway:	n/a	n/a
30	CTCF	chr1:155978540-155978690	HCT-116	colon:	n/a	n/a
31	POLR2A	chr1:155978279-155978801	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155965947..155968547-chr1:155977154..155978794,2	K562	blood:
2	chr1:155977756..155980066-chr1:155982576..155985568,2	MCF-7	breast:
3	chr1:155978414..155980525-chr1:156022299..156025180,2	K562	blood:
4	chr1:155977027..155979132-chr1:156029472..156031221,2	MCF-7	breast:
5	chr1:155906562..155909421-chr1:155978385..155980354,2	K562	blood:
6	chr1:155978402..155979208-chr1:155990515..155991136,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000132698	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000116586	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1111102	0.82[YRI][hapmap]
rs11577179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582305	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12032631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043212	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12128541	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1475766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17381047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385065	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966243	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2095402	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297792	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364400	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364401	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2886070	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34126883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34444588	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34995046	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4330912	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4661079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668204	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517202	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10908486	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155971400-155978600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:155971400-155978600	Weak transcription	NHDF-Ad	bronchial
3	chr1:155971600-155978600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:155971800-155978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:155972000-155978600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:155972400-155978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:155973600-155978600	Weak transcription	NH-A	brain
8	chr1:155973800-155978600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:155973800-155978600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:155973800-155989400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:155975000-155978600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:155975000-155978600	Weak transcription	Colonic Mucosa	Colon
13	chr1:155975000-155978600	Weak transcription	GM12878-XiMat	blood
14	chr1:155975400-155978600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:155975400-155978600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:155975400-155978600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:155975400-155979200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:155975600-155979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:155975600-155980400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:155976000-155978600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:155976000-155989600	Strong transcription	Fetal Stomach	stomach
22	chr1:155976200-155988800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:155976600-155978600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:155976600-155982400	Strong transcription	Spleen	Spleen
25	chr1:155976600-155985000	Strong transcription	Lung	lung
26	chr1:155976600-155985400	Strong transcription	Thymus	Thymus
27	chr1:155976600-155988400	Strong transcription	Liver	Liver
28	chr1:155976600-155988400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:155976600-155988600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:155976600-155988800	Strong transcription	Fetal Intestine Small	intestine
31	chr1:155976600-155989200	Strong transcription	Fetal Intestine Large	intestine
32	chr1:155976600-155989400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:155976800-155985000	Strong transcription	Fetal Brain Female	brain
34	chr1:155976800-155985400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:155976800-155989400	Strong transcription	Fetal Thymus	thymus
36	chr1:155976800-155989600	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:155977000-155978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:155977000-155978600	Weak transcription	Gastric	stomach
39	chr1:155977000-155980400	Weak transcription	Fetal Brain Male	brain
40	chr1:155977200-155978600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:155977200-155978600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:155977200-155978600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:155977200-155978600	Weak transcription	Stomach Mucosa	stomach
44	chr1:155977200-155983400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:155977200-155987000	Weak transcription	Fetal Heart	heart
46	chr1:155977200-155989200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:155978000-155979000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:155978000-155983800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:155978200-155978600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:155978200-155978600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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