Variant report

Variant	rs6704872
Chromosome Location	chr2:48124070-48124071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48123997..48126894-chr2:48127271..48129430,2	MCF-7	breast:
2	chr2:48115404..48116936-chr2:48122122..48124133,2	K562	blood:
3	chr2:48122264..48126489-chr2:48130939..48134880,5	MCF-7	breast:
4	chr2:48123308..48125922-chr2:48127457..48129579,2	K562	blood:
5	chr2:48120242..48124269-chr2:48131325..48134393,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138081	Chromatin interaction
ENSG00000233230	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10490303	0.88[GIH][hapmap]
rs10495947	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10495948	0.88[GIH][hapmap]
rs17036996	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17037002	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17037018	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17037021	0.88[GIH][hapmap]
rs17037038	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17037040	1.00[GIH][hapmap]
rs17037055	0.91[YRI][hapmap]
rs17037064	0.82[YRI][hapmap]
rs2134056	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4381823	0.88[GIH][hapmap]
rs60154625	0.87[EUR][1000 genomes]
rs60866242	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6714441	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6723441	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73929251	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7572674	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7587289	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv523013	chr2:48073117-48146122	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv874000	chr2:48078838-48291582	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6704872	PREPL	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48095200-48127200	Weak transcription	Fetal Kidney	kidney
2	chr2:48095400-48129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:48098400-48125000	Weak transcription	HUVEC	blood vessel
4	chr2:48098600-48129000	Weak transcription	Gastric	stomach
5	chr2:48098600-48129000	Weak transcription	Pancreas	Pancrea
6	chr2:48100600-48129200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:48108600-48129800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:48110200-48125200	Weak transcription	Brain Germinal Matrix	brain
9	chr2:48110600-48127000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:48110600-48130800	Weak transcription	Fetal Thymus	thymus
11	chr2:48111000-48130800	Weak transcription	Thymus	Thymus
12	chr2:48111600-48127000	Weak transcription	Fetal Intestine Large	intestine
13	chr2:48112800-48127200	Weak transcription	Right Atrium	heart
14	chr2:48114400-48129000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:48114400-48130600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:48115000-48131000	Weak transcription	Stomach Mucosa	stomach
17	chr2:48115200-48124400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:48115200-48131400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:48115400-48125200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:48115400-48125600	Weak transcription	Dnd41	blood
21	chr2:48116200-48125200	Weak transcription	HSMM	muscle
22	chr2:48117000-48129200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:48117800-48125000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:48118000-48127000	Weak transcription	Placenta	Placenta
25	chr2:48118200-48127200	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:48118200-48131000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:48118400-48125600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:48118400-48127600	Enhancers	Primary T cells from cord blood	blood
29	chr2:48118600-48127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:48119000-48127800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:48119600-48124200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:48119600-48127200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:48119600-48130200	Weak transcription	HMEC	breast
34	chr2:48119800-48124400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:48119800-48124800	Weak transcription	NHEK	skin
36	chr2:48119800-48125200	Weak transcription	NH-A	brain
37	chr2:48119800-48125400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:48119800-48127000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:48120000-48124400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:48120000-48124400	Weak transcription	NHDF-Ad	bronchial
41	chr2:48120000-48125600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:48120000-48126800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:48120200-48124800	Weak transcription	NHLF	lung
44	chr2:48120200-48125000	Weak transcription	Osteobl	bone
45	chr2:48120200-48130400	Weak transcription	Psoas Muscle	Psoas
46	chr2:48120400-48124600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr2:48120800-48126000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:48120800-48126200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr2:48120800-48130400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr2:48121000-48125400	Enhancers	HUES48 Cell Line	embryonic stem cell

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