Variant report

Variant	rs4656942
Chromosome Location	chr1:160831048-160831049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LY9-2	chr1:160830898-160831203	expReg_chr1_18595_+

Extended variants
information (count: 11 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11265492	0.91[AFR][1000 genomes]
rs12117689	0.91[AFR][1000 genomes]
rs12143580	0.82[AFR][1000 genomes]
rs1556517	0.91[AFR][1000 genomes]
rs2274906	1.00[YRI][hapmap]
rs3904492	1.00[LWK][hapmap]
rs4656271	0.91[AFR][1000 genomes]
rs4656932	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4656942	FCGR2A	cis	cerebellum	SCAN
rs4656942	ISG20L2	cis	cerebellum	SCAN
rs4656942	OR10X1	cis	cerebellum	SCAN
rs4656942	PFDN2	cis	cerebellum	SCAN
rs4656942	C1orf192	cis	cerebellum	SCAN
rs4656942	SPTA1	cis	parietal	SCAN
rs4656942	PPOX	cis	cerebellum	SCAN
rs4656942	ISG20L2	cis	parietal	SCAN
rs4656942	ROBLD3	cis	cerebellum	SCAN
rs4656942	CD244	Cis_1M	lymphoblastoid	RTeQTL
rs4656942	MRPL24	cis	parietal	SCAN
rs4656942	LMNA	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160824600-160831200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:160826400-160831800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:160826600-160832200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:160828600-160832200	Weak transcription	Right Atrium	heart
5	chr1:160828600-160835000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:160828800-160832000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:160829000-160831800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:160829200-160832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:160830000-160833000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:160830000-160833200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:160830000-160833800	Enhancers	Primary B cells from cord blood	blood
12	chr1:160830200-160831200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:160830200-160834200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:160830600-160831200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:160830600-160831200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:160830600-160831200	Flanking Active TSS	Liver	Liver
17	chr1:160830600-160831400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:160830600-160832600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:160830600-160833000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:160830600-160833000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:160830600-160833600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr1:160830800-160831200	Bivalent Enhancer	Adipose Nuclei	Adipose
23	chr1:160830800-160831800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:160830800-160832000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:160830800-160832600	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr1:160830800-160832600	Enhancers	Spleen	Spleen
27	chr1:160830800-160832800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:160831000-160831200	Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:160831000-160831400	Enhancers	Colonic Mucosa	Colon
30	chr1:160831000-160831800	Weak transcription	Duodenum Mucosa	Duodenum

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