Variant report

Variant	rs4848993
Chromosome Location	chr2:112830165-112830166
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	chr2:112826096..112827842-chr2:112829800..112832394,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10165845	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10175143	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10178449	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10182333	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045300	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs10779884	0.95[ASN][1000 genomes]
rs10864898	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618637	0.88[ASN][1000 genomes]
rs4241121	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4257409	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4613287	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4849007	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849044	0.88[ASN][1000 genomes]
rs6707397	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs6730057	0.97[ASN][1000 genomes]
rs6731563	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6737707	0.86[CHD][hapmap];0.83[MEX][hapmap]
rs7577442	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7580507	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7581849	0.90[JPT][hapmap]
rs7591702	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595574	0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9308669	0.82[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9653401	0.88[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9653422	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv829620	chr2:112825846-112832456	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4848993	CCDC138	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814200-112835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:112814200-112849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:112814400-112831600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:112814800-112832200	Weak transcription	A549	lung
6	chr2:112814800-112842000	Weak transcription	Fetal Heart	heart
7	chr2:112815200-112833200	Weak transcription	Hela-S3	cervix
8	chr2:112816000-112833800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:112816600-112834200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:112817000-112830200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:112817400-112835400	Weak transcription	Esophagus	oesophagus
14	chr2:112817400-112835400	Weak transcription	Right Ventricle	heart
15	chr2:112818600-112833800	Strong transcription	Primary T cells from cord blood	blood
16	chr2:112818600-112836600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:112818800-112834000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:112819200-112838200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:112819600-112836400	Strong transcription	Fetal Intestine Large	intestine
20	chr2:112820400-112831000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:112820400-112847000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:112821200-112831200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:112821400-112835400	Weak transcription	Gastric	stomach
24	chr2:112821400-112835400	Weak transcription	Ovary	ovary
25	chr2:112821400-112835400	Weak transcription	Spleen	Spleen
26	chr2:112821400-112849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:112821600-112841600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:112822200-112831000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:112822200-112854400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:112822400-112835200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:112822800-112835400	Weak transcription	Pancreas	Pancrea
32	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:112823400-112835200	Weak transcription	Thymus	Thymus
34	chr2:112823600-112831800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:112823600-112844200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:112824200-112830600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:112824200-112833000	Weak transcription	NHLF	lung
38	chr2:112824200-112833200	Weak transcription	HSMMtube	muscle
39	chr2:112824200-112844000	Weak transcription	Fetal Brain Male	brain
40	chr2:112825000-112831000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:112825000-112831600	Weak transcription	HMEC	breast
42	chr2:112825000-112838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:112825400-112831600	Weak transcription	NHDF-Ad	bronchial
44	chr2:112825400-112838800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:112825600-112831000	Weak transcription	K562	blood
46	chr2:112825600-112831600	Weak transcription	Small Intestine	intestine
47	chr2:112825600-112831600	Weak transcription	Stomach Mucosa	stomach
48	chr2:112825600-112835200	Weak transcription	Left Ventricle	heart
49	chr2:112825600-112835200	Weak transcription	Lung	lung
50	chr2:112825600-112835200	Weak transcription	Rectal Smooth Muscle	rectum

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