Variant report

Variant	rs4656941
Chromosome Location	chr1:160830317-160830318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160829381..160830881-chr5:89705288..89707065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255647	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10908807	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11265498	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265499	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265500	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11265501	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12035295	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035537	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12036607	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12036670	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12037395	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12037740	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037885	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12038419	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12038600	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039896	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039959	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040060	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040152	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040750	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12046019	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12046021	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047127	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12048113	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1412849	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1576964	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1855188	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1855189	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766378	0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656940	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656943	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs480104	0.81[ASN][1000 genomes]
rs57483437	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58418513	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59712018	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61803263	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61803285	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698454	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72710762	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7410867	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7412693	0.84[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7412696	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7419088	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7419110	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7419145	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs955370	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs955371	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656941	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160821000-160830800	Weak transcription	Spleen	Spleen
2	chr1:160824600-160831200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:160825200-160830600	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:160826400-160830600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:160826400-160830800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:160826400-160831800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:160826600-160830400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:160826600-160832200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:160827000-160830600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:160828400-160830600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:160828600-160832200	Weak transcription	Right Atrium	heart
12	chr1:160828600-160835000	Weak transcription	Fetal Intestine Large	intestine
13	chr1:160828800-160832000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr1:160829000-160830600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:160829000-160830800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:160829000-160831800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:160829200-160830800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:160829200-160831000	Weak transcription	Colonic Mucosa	Colon
19	chr1:160829200-160832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:160829800-160830800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:160830000-160830400	Weak transcription	Adipose Nuclei	Adipose
22	chr1:160830000-160830600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:160830000-160833000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr1:160830000-160833200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:160830000-160833800	Enhancers	Primary B cells from cord blood	blood
26	chr1:160830200-160830600	Enhancers	Liver	Liver
27	chr1:160830200-160831200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:160830200-160834200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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