Variant report

Variant	rs11681508
Chromosome Location	chr2:55343965-55343966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:55342362-55344019	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
2	JUND	chr2:55342457-55343976	K562	blood:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
3	ZNF384	chr2:55343808-55344151	K562	blood:	n/a	n/a
4	RCOR1	chr2:55342434-55344020	K562	blood:	n/a	n/a
5	JUND	chr2:55342314-55344001	SK-N-SH	brain:	n/a	chr2:55343035-55343045 chr2:55343036-55343043 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045 chr2:55343036-55343044 chr2:55343035-55343045
6	GATA1	chr2:55341662-55344054	K562	blood:	n/a	chr2:55343402-55343414 chr2:55343403-55343412 chr2:55342694-55342710

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55343511..55346556-chr2:55364762..55366710,3	K562	blood:
3	chr2:55278333..55279964-chr2:55343174..55345064,2	MCF-7	breast:
4	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
5	chr2:55251702..55254676-chr2:55343936..55346646,2	K562	blood:
6	chr2:55341952..55344762-chr2:55357897..55359885,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10168457	0.96[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10496039	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11692696	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990261	0.82[ASN][1000 genomes]
rs13006159	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4672016	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11681508	FLJ31438	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55339600-55345800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:55339600-55345800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:55339600-55345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:55339600-55346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:55339600-55347000	Weak transcription	Left Ventricle	heart
8	chr2:55339800-55344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55339800-55345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:55339800-55345800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:55339800-55347000	Weak transcription	Lung	lung
12	chr2:55340000-55345600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:55340200-55346200	Weak transcription	Fetal Brain Female	brain
14	chr2:55340400-55344200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:55340400-55345800	Enhancers	K562	blood
16	chr2:55340600-55344400	Weak transcription	Brain Germinal Matrix	brain
17	chr2:55340600-55345200	Weak transcription	Fetal Brain Male	brain
18	chr2:55340600-55347000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:55340800-55344600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:55340800-55345600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:55340800-55346000	Weak transcription	Spleen	Spleen
22	chr2:55340800-55347200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:55340800-55348000	Enhancers	Brain Hippocampus Middle	brain
24	chr2:55340800-55348000	Enhancers	Brain Substantia Nigra	brain
25	chr2:55341000-55345800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:55341000-55346000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:55341000-55346800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:55341000-55346800	Weak transcription	Placenta	Placenta
29	chr2:55341200-55344400	Weak transcription	Brain Angular Gyrus	brain
30	chr2:55341200-55345600	Weak transcription	Primary B cells from cord blood	blood
31	chr2:55341200-55345800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr2:55341200-55346200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:55341200-55346800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:55341200-55347000	Weak transcription	Stomach Mucosa	stomach
35	chr2:55341400-55345800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:55341600-55345800	Weak transcription	Fetal Thymus	thymus
37	chr2:55341800-55344400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:55341800-55344600	Enhancers	NHDF-Ad	bronchial
39	chr2:55342200-55346200	Enhancers	Hela-S3	cervix
40	chr2:55342200-55347000	Enhancers	HSMMtube	muscle
41	chr2:55342400-55350200	Enhancers	Fetal Heart	heart
42	chr2:55342600-55344000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:55342600-55344600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:55342600-55344600	Enhancers	NHEK	skin
45	chr2:55342800-55344200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:55343000-55344600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:55343000-55345400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:55343000-55346000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:55343200-55344400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:55343200-55344800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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