Variant report

Variant	rs4671950
Chromosome Location	chr2:54759730-54759731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54759032..54761078-chr2:54799312..54800939,2	MCF-7	breast:
2	chr2:54196354..54198285-chr2:54758115..54760291,3	MCF-7	breast:
3	chr2:54758614..54760270-chr2:54799626..54801180,2	MCF-7	breast:
4	chr2:54759443..54762729-chr2:54766620..54769498,3	MCF-7	breast:
5	chr2:54752145..54754517-chr2:54758567..54761057,2	MCF-7	breast:
6	chr2:54759200..54761130-chr2:54762739..54764614,2	K562	blood:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000228108	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10165490	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047499	0.80[TSI][hapmap]
rs11895933	0.82[LWK][hapmap]
rs11898012	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs12104998	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12105792	0.80[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12617036	0.84[EUR][1000 genomes]
rs13016942	0.80[CHB][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs13399435	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs1367295	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17344044	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs17344072	0.80[CHB][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs17521078	0.85[JPT][hapmap];0.89[TSI][hapmap]
rs1802889	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864493	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2941595	0.86[TSI][hapmap]
rs2971877	0.80[TSI][hapmap]
rs2971879	0.86[TSI][hapmap]
rs3936082	0.85[YRI][hapmap]
rs4233952	0.82[ASN][1000 genomes]
rs4233954	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514917	0.97[ASN][1000 genomes]
rs4514918	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592889	0.84[EUR][1000 genomes]
rs4671221	0.82[CEU][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs4671222	0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs4671225	0.80[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs4671226	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671945	0.85[JPT][hapmap]
rs4671946	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671947	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671949	0.85[EUR][1000 genomes]
rs4671951	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4671953	0.93[EUR][1000 genomes]
rs4671954	0.96[EUR][1000 genomes]
rs4671956	0.80[CHB][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4671960	0.83[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4671961	0.83[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4990319	0.83[EUR][1000 genomes]
rs56381959	0.82[ASN][1000 genomes]
rs6545411	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs6545415	0.85[JPT][hapmap];0.83[TSI][hapmap]
rs6545419	0.85[JPT][hapmap]
rs6545420	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545421	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545427	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs6545429	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs6704769	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6724590	0.90[ASN][1000 genomes]
rs6729826	0.88[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6746016	0.90[JPT][hapmap]
rs6761369	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs6761398	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7558950	0.85[EUR][1000 genomes]
rs7589236	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671950	EML6	cis	Thyroid	GTEx
rs4671950	SPTBN1	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 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	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
10	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
13	chr2:54752000-54764600	Weak transcription	Gastric	stomach
14	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:54752600-54759800	Weak transcription	GM12878-XiMat	blood
17	chr2:54753200-54759800	Strong transcription	Adipose Nuclei	Adipose
18	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:54754000-54760200	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:54754400-54759800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:54754600-54760000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:54755000-54761000	Weak transcription	Right Ventricle	heart
26	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:54755200-54759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:54755400-54762600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr2:54755600-54761200	Weak transcription	Fetal Brain Male	brain
30	chr2:54756400-54759800	Strong transcription	HSMMtube	muscle
31	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
32	chr2:54756800-54759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:54756800-54763200	Enhancers	Fetal Intestine Large	intestine
34	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:54757000-54761000	Enhancers	Fetal Intestine Small	intestine
36	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:54757200-54761200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:54757400-54759800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:54757400-54760400	Weak transcription	Fetal Kidney	kidney
41	chr2:54757400-54761200	Weak transcription	Fetal Brain Female	brain
42	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:54757800-54762000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:54758000-54760200	Enhancers	NH-A	brain
46	chr2:54758000-54760400	Enhancers	HUVEC	blood vessel
47	chr2:54758000-54760800	Enhancers	NHDF-Ad	bronchial
48	chr2:54758000-54760800	Enhancers	Osteobl	bone
49	chr2:54758000-54761600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:54758000-54762000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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