Variant report

Variant	rs1246942
Chromosome Location	chr6:4974320-4974321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NANOG	chr6:4974220-4974560	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA3	chr6:4974250-4974624	T-47D	breast:	n/a	n/a
3	NR2F2	chr6:4974284-4974695	MCF-7	breast:	n/a	n/a
4	TAF1	chr6:4974199-4974674	ECC-1	luminal epithelium:	n/a	n/a
5	TAF1	chr6:4974095-4974590	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr6:4974252-4974715	ECC-1	luminal epithelium:	n/a	chr6:4974283-4974293
7	POLR2A	chr6:4973955-4974709	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:4974163-4974688	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr6:4974138-4974510	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF7	chr6:4974127-4974588	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:4974208-4974457	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:4974161-4974505	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr6:4974203-4974599	H1-hESC	embryonic stem cell:	n/a	n/a
14	NFIC	chr6:4974251-4975210	ECC-1	luminal epithelium:	n/a	chr6:4974924-4974941 chr6:4974925-4974941
15	HCFC1	chr6:4974281-4974467	K562	blood:	n/a	n/a
16	UBTF	chr6:4974275-4974575	K562	blood:	n/a	n/a
17	NFIC	chr6:4974234-4975303	ECC-1	luminal epithelium:	n/a	chr6:4974924-4974941 chr6:4974925-4974941
18	CEBPB	chr6:4974146-4974607	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:4974196-4974544	H1-hESC	embryonic stem cell:	n/a	n/a
20	GABPA	chr6:4974261-4974593	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4973208..4976240-chr6:4987607..4989532,3	MCF-7	breast:
2	chr6:4972160..4974386-chr6:4980917..4982666,2	K562	blood:

Variant related genes	Relation type
ENSG00000217030	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1246941	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1246948	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246950	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246951	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1246952	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246978	0.81[ASN][1000 genomes]
rs1246979	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246980	0.81[ASN][1000 genomes]
rs1246981	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246983	0.81[ASN][1000 genomes]
rs1246986	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs166694	0.81[ASN][1000 genomes]
rs1749143	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1749145	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1749147	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2477486	0.81[ASN][1000 genomes]
rs2477487	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs275232	0.81[ASN][1000 genomes]
rs275233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275234	0.81[ASN][1000 genomes]
rs275235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275236	0.81[ASN][1000 genomes]
rs275237	0.81[ASN][1000 genomes]
rs275238	0.81[ASN][1000 genomes]
rs275239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275243	0.81[ASN][1000 genomes]
rs275244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275245	0.81[ASN][1000 genomes]
rs275246	0.81[ASN][1000 genomes]
rs275248	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs275249	0.81[ASN][1000 genomes]
rs275250	0.81[ASN][1000 genomes]
rs275251	0.81[ASN][1000 genomes]
rs275252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs275254	0.81[ASN][1000 genomes]
rs275255	0.81[ASN][1000 genomes]
rs275256	0.81[ASN][1000 genomes]
rs275257	0.81[ASN][1000 genomes]
rs275258	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs275259	0.81[ASN][1000 genomes]
rs439795	0.85[CEU][hapmap];0.91[CHB][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs563620	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs808733	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9405250	0.81[ASN][1000 genomes]
rs9405789	0.81[ASN][1000 genomes]
rs9405790	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1246942	RPP40	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4971400-4975000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:4972200-4974600	Weak transcription	Fetal Brain Female	brain
3	chr6:4973600-4975000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:4973600-4975000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:4973600-4975200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:4973600-4975800	Enhancers	Fetal Muscle Leg	muscle
7	chr6:4973800-4974400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:4973800-4974400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:4973800-4974400	Enhancers	Brain Germinal Matrix	brain
10	chr6:4973800-4974400	Enhancers	Colon Smooth Muscle	Colon
11	chr6:4973800-4974600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:4973800-4974600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:4973800-4975000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:4973800-4975000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:4973800-4975200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:4973800-4975200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:4973800-4975200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:4973800-4975200	Enhancers	Adipose Nuclei	Adipose
19	chr6:4973800-4975400	Enhancers	Stomach Smooth Muscle	stomach
20	chr6:4973800-4975600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:4973800-4975600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:4973800-4975600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:4973800-4975600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:4973800-4975600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:4973800-4975600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:4973800-4975600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:4973800-4975600	Enhancers	Fetal Muscle Trunk	muscle
28	chr6:4973800-4975600	Enhancers	Psoas Muscle	Psoas
29	chr6:4973800-4975800	Enhancers	Fetal Stomach	stomach
30	chr6:4974000-4974400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr6:4974000-4974800	Enhancers	Fetal Lung	lung
32	chr6:4974000-4974800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr6:4974000-4974800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr6:4974000-4975000	Enhancers	HSMMtube	muscle
35	chr6:4974000-4975400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:4974000-4976000	Enhancers	Fetal Brain Male	brain
37	chr6:4974200-4974400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr6:4974200-4974400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:4974200-4974400	Bivalent Enhancer	Spleen	Spleen
40	chr6:4974200-4974600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:4974200-4974600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:4974200-4974600	Enhancers	Left Ventricle	heart
43	chr6:4974200-4975000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:4974200-4975400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:4974200-4975600	Enhancers	Rectal Smooth Muscle	rectum

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