Variant report

Variant	rs1111102
Chromosome Location	chr1:155993456-155993457
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:155993405-155993584	Hela-S3	cervix:	n/a	n/a
2	REST	chr1:155993320-155993608	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:155987340..155997180-chr1:156020881..156026682,16	K562	blood:
2	chr1:155993386..155995708-chr1:156048411..156050502,2	MCF-7	breast:
3	chr1:155989047..155993552-chr1:156021675..156026301,17	MCF-7	breast:
4	chr1:155990929..155994838-chr1:156000466..156003065,3	K562	blood:
5	chr1:155988173..156003032-chr1:156020965..156026206,23	MCF-7	breast:
6	chr1:155902781..155905486-chr1:155988342..155993651,4	K562	blood:

No data

Variant related genes	Relation type
SSR2	TF binding region
ENSG00000116586	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10796955	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs10908486	0.82[YRI][hapmap]
rs11264426	0.86[CEU][hapmap]
rs11486142	0.80[EUR][1000 genomes]
rs11585845	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs12037177	0.81[CEU][hapmap]
rs12118795	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs12568523	0.80[CEU][hapmap]
rs1475766	0.82[YRI][hapmap]
rs1889532	0.86[CEU][hapmap]
rs2016251	0.81[CEU][hapmap]
rs2282301	0.81[CEU][hapmap]
rs2297649	0.81[CEU][hapmap]
rs3820592	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4661218	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs59781317	0.81[EUR][1000 genomes]
rs6427297	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667652	0.81[CEU][hapmap]
rs6670493	0.85[CEU][hapmap]
rs6696019	0.81[CEU][hapmap]
rs72708238	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72708239	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7534858	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs867549	0.81[CEU][hapmap]
rs867550	0.81[CEU][hapmap]
rs915178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs915181	0.81[CEU][hapmap]
rs928596	0.86[CEU][hapmap];0.82[TSI][hapmap]

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
rs1111102	PRUNE	cis	cerebellum	SCAN
rs1111102	YY1AP1	cis	cerebellum	SCAN
rs1111102	ROBLD3	cis	parietal	SCAN
rs1111102	RIT1	cis	cerebellum	SCAN
rs1111102	RORC	cis	cerebellum	SCAN
rs1111102	SNX27	cis	parietal	SCAN
rs1111102	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155990800-155995800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:155990800-156006000	Weak transcription	Spleen	Spleen
3	chr1:155990800-156006800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:155991000-155995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:155991000-155995600	Weak transcription	Placenta	Placenta
6	chr1:155991000-155995800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:155991000-156002600	Weak transcription	NHLF	lung
8	chr1:155991000-156005800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:155991000-156011600	Weak transcription	Colonic Mucosa	Colon
10	chr1:155991200-155994200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:155991200-155994200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:155991200-155994400	Weak transcription	HepG2	liver
13	chr1:155991200-155995000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:155991200-155995600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:155991200-155995600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:155991200-155995800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:155991200-155995800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:155991200-155995800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:155991200-155995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:155991200-155995800	Weak transcription	A549	lung
21	chr1:155991200-155995800	Weak transcription	HMEC	breast
22	chr1:155991200-155995800	Weak transcription	HUVEC	blood vessel
23	chr1:155991200-156002800	Weak transcription	NH-A	brain
24	chr1:155991200-156005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:155991200-156005600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:155991200-156005800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:155991200-156005800	Weak transcription	Liver	Liver
28	chr1:155991200-156005800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:155991200-156005800	Weak transcription	Fetal Thymus	thymus
30	chr1:155991200-156006000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:155991200-156006000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:155991200-156006600	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:155991200-156006600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:155991200-156010800	Weak transcription	Fetal Heart	heart
35	chr1:155991200-156020000	Weak transcription	GM12878-XiMat	blood
36	chr1:155991800-155994800	Weak transcription	K562	blood
37	chr1:155992200-156005800	Weak transcription	Dnd41	blood

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