Variant report

Variant	rs1568673
Chromosome Location	chr2:152690248-152690249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152684180..152686852-chr2:152690162..152693530,4	MCF-7	breast:
2	chr2:152689042..152691234-chr2:152692225..152695696,3	K562	blood:
3	chr2:152688578..152690368-chr2:152697278..152699911,2	K562	blood:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11680834	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs13005519	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs3820705	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4303715	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6433656	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7609344	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv3436133	chr2:152686106-152690504	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1568673	ROM1	trans	brain	seeQTL
rs1568673	FSTL3	trans	brain	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152685400-152697200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:152685600-152694600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:152685600-152695200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:152685600-152697600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:152685600-152699400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:152685600-152709600	Weak transcription	Fetal Brain Female	brain
7	chr2:152685800-152690400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:152685800-152690400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:152685800-152690400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:152685800-152690400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:152685800-152690400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:152685800-152690400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:152685800-152692000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:152685800-152695200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:152685800-152695600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:152685800-152697400	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:152685800-152699200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:152685800-152699400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:152685800-152702200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:152687600-152696600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:152688000-152697600	Weak transcription	HepG2	liver
22	chr2:152688200-152691400	Weak transcription	Fetal Intestine Large	intestine
23	chr2:152689800-152692200	Enhancers	GM12878-XiMat	blood
24	chr2:152690000-152692400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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