Variant report

Variant	rs6554096
Chromosome Location	chr4:54229286-54229287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54220179..54222765-chr4:54228443..54230623,2	K562	blood:
2	chr4:54225875..54227419-chr4:54229221..54231130,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10012853	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10013573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10028214	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1014056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10517291	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs10517292	0.86[CHB][hapmap]
rs10517296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11935822	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942086	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946199	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12499401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12501431	0.81[EUR][1000 genomes]
rs12507723	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13125807	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130836	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1351514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514387	0.96[YRI][hapmap]
rs1514388	0.96[YRI][hapmap]
rs1514389	0.96[YRI][hapmap]
rs17082565	0.85[CHB][hapmap]
rs17082659	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17082910	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2128103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2170421	0.88[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271555	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271557	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2292579	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs34028346	0.82[EUR][1000 genomes]
rs34173240	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34317954	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35033239	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35089532	0.82[EUR][1000 genomes]
rs35225781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35313782	0.82[EUR][1000 genomes]
rs3817270	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3946758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3986364	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864451	0.86[CHB][hapmap]
rs4864453	0.85[CHB][hapmap]
rs4864747	0.85[CHB][hapmap]
rs6420001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554095	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554099	0.83[JPT][hapmap];0.81[YRI][hapmap]
rs6554102	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6554103	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554107	0.82[EUR][1000 genomes]
rs6554108	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6826467	0.85[CHB][hapmap]
rs6846569	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847289	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852884	0.84[YRI][hapmap]
rs71597836	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751265	0.85[CHB][hapmap]
rs7678953	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7679743	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7684450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7684894	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694840	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967018	1.00[YRI][hapmap]
rs980988	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997832	0.84[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9997358	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9997844	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6554096	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:54188200-54231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:54213800-54230400	Weak transcription	Fetal Kidney	kidney
4	chr4:54214000-54230800	Weak transcription	Aorta	Aorta
5	chr4:54214000-54231200	Weak transcription	Lung	lung
6	chr4:54214200-54230000	Weak transcription	Fetal Heart	heart
7	chr4:54214200-54230000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:54214200-54230400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:54214200-54230800	Weak transcription	Brain Angular Gyrus	brain
10	chr4:54214200-54230800	Weak transcription	Brain Substantia Nigra	brain
11	chr4:54214200-54230800	Weak transcription	Fetal Lung	lung
12	chr4:54214200-54230800	Weak transcription	Right Ventricle	heart
13	chr4:54214200-54230800	Weak transcription	HSMMtube	muscle
14	chr4:54214200-54231000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:54214200-54231000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:54214200-54231200	Weak transcription	Spleen	Spleen
17	chr4:54214400-54230200	Weak transcription	HMEC	breast
18	chr4:54214600-54230000	Weak transcription	Brain Anterior Caudate	brain
19	chr4:54214800-54230200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:54218800-54230800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:54219200-54229400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:54219200-54229400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:54219200-54230000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:54219400-54229400	Weak transcription	Left Ventricle	heart
25	chr4:54219400-54230400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:54219400-54230800	Weak transcription	Thymus	Thymus
27	chr4:54219600-54230000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr4:54219600-54230200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:54219800-54230400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:54220400-54230400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:54220400-54230800	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:54220600-54230800	Weak transcription	Fetal Thymus	thymus
33	chr4:54220800-54230400	Weak transcription	Fetal Intestine Large	intestine
34	chr4:54221200-54230800	Weak transcription	Fetal Intestine Small	intestine
35	chr4:54222400-54230800	Weak transcription	Psoas Muscle	Psoas
36	chr4:54224800-54233000	Active TSS	GM12878-XiMat	blood
37	chr4:54226200-54231200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr4:54226400-54230800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:54226800-54231200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr4:54227200-54229400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:54227200-54231000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:54227400-54229600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:54227400-54230000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:54227400-54230000	Enhancers	Primary T cells from cord blood	blood
45	chr4:54227400-54230800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:54227600-54229400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:54227600-54229400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:54227600-54229400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:54227600-54229800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:54227600-54230000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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