Variant report

Variant	rs10165490
Chromosome Location	chr2:54761533-54761534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54760402..54763033-chr2:54763448..54765136,2	MCF-7	breast:
2	chr2:54759443..54762729-chr2:54766620..54769498,3	MCF-7	breast:
3	chr2:54761267..54763626-chr2:54824184..54826863,2	K562	blood:
4	chr2:54761132..54763342-chr2:54783145..54786144,3	MCF-7	breast:
5	chr2:54761029..54763821-chr2:54783036..54786331,4	K562	blood:

Variant related genes	Relation type
ENSG00000228108	Chromatin interaction
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10180713	1.00[YRI][hapmap]
rs1047499	1.00[YRI][hapmap]
rs11892788	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11898012	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12104998	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs12105792	0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12617036	0.84[EUR][1000 genomes]
rs13016942	0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs13399435	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1367295	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17344044	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17344072	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs17521078	0.85[JPT][hapmap]
rs1802889	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864493	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2941586	1.00[YRI][hapmap]
rs2941587	1.00[YRI][hapmap]
rs2941595	1.00[YRI][hapmap]
rs2971877	1.00[YRI][hapmap]
rs2971879	1.00[YRI][hapmap]
rs4233952	0.82[ASN][1000 genomes]
rs4233954	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514917	0.97[ASN][1000 genomes]
rs4514918	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592889	0.84[EUR][1000 genomes]
rs4671221	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs4671222	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs4671225	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4671226	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671945	0.86[JPT][hapmap]
rs4671946	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671947	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671949	0.85[EUR][1000 genomes]
rs4671950	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671951	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4671953	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671954	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671956	0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4671960	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs4671961	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs4990319	0.83[EUR][1000 genomes]
rs56381959	0.82[ASN][1000 genomes]
rs6545411	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6545415	0.85[JPT][hapmap]
rs6545419	0.80[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs6545420	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545421	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545427	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6545429	0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6545434	1.00[YRI][hapmap]
rs6704769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6724590	0.90[ASN][1000 genomes]
rs6729826	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs6732949	1.00[YRI][hapmap]
rs6746016	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6761369	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6761398	0.80[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7558950	0.85[EUR][1000 genomes]
rs7589236	0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10165490	EML6	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
9	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:54752000-54764600	Weak transcription	Gastric	stomach
11	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
15	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:54755400-54762600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
20	chr2:54756800-54763200	Enhancers	Fetal Intestine Large	intestine
21	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
24	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:54757800-54762000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:54758000-54761600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:54758000-54762000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:54758000-54762400	Enhancers	HMEC	breast
30	chr2:54758000-54762600	Enhancers	Brain Substantia Nigra	brain
31	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
32	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:54758800-54762000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:54758800-54762000	Weak transcription	Aorta	Aorta
35	chr2:54758800-54762400	Enhancers	Brain Anterior Caudate	brain
36	chr2:54759200-54762200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr2:54759400-54763000	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr2:54759600-54761800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:54759600-54762200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:54759600-54762200	Enhancers	Brain Hippocampus Middle	brain
41	chr2:54759600-54762200	Enhancers	Stomach Mucosa	stomach
42	chr2:54759600-54762400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:54759600-54763800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:54759600-54764000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:54759800-54761800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:54759800-54762200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:54760200-54761600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr2:54760200-54768800	Genic enhancers	Left Ventricle	heart
49	chr2:54760400-54761800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:54760400-54761800	Weak transcription	NHLF	lung

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