Variant report

Variant	rs2294143
Chromosome Location	chr8:8413380-8413381
allele	A/G
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	JUND	chr8:8412569-8413577	SK-N-SH	brain:	n/a	chr8:8413064-8413072 chr8:8413063-8413073
2	MAX	chr8:8412816-8413552	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr8:8412602-8414319	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr8:8412717-8413553	SK-N-SH	brain:	n/a	n/a
5	EP300	chr8:8412731-8413410	SK-N-SH_RA	brain:	n/a	chr8:8412824-8412838
6	RXRA	chr8:8412855-8413499	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr8:8412478-8413560	SK-N-SH	brain:	n/a	n/a
8	JUND	chr8:8412684-8413565	SK-N-SH	brain:	n/a	chr8:8413064-8413072 chr8:8413063-8413073
9	POLR2A	chr8:8412365-8413465	PFSK-1	brain:	n/a	n/a
10	YY1	chr8:8412949-8413445	SK-N-SH_RA	brain:	n/a	chr8:8413328-8413337
11	SIN3AK20	chr8:8412607-8413430	SK-N-SH	brain:	n/a	n/a
12	PBX3	chr8:8412556-8413527	SK-N-SH	brain:	n/a	n/a
13	FOSL2	chr8:8412856-8413455	SK-N-SH	brain:	n/a	chr8:8413064-8413072 chr8:8413063-8413073
14	RAD21	chr8:8412790-8413416	SK-N-SH_RA	brain:	n/a	n/a
15	EP300	chr8:8412402-8414337	SK-N-SH	brain:	n/a	chr8:8412824-8412838
16	YY1	chr8:8413005-8413495	SK-N-SH_RA	brain:	n/a	chr8:8413328-8413337
17	FOXM1	chr8:8412562-8414219	SK-N-SH	brain:	n/a	n/a
18	SIN3AK20	chr8:8412738-8413463	MCF-7	breast:	n/a	n/a
19	POLR2A	chr8:8412528-8413412	PFSK-1	brain:	n/a	n/a
20	MEF2A	chr8:8412697-8413503	SK-N-SH	brain:	n/a	chr8:8413064-8413072
21	EP300	chr8:8412791-8413441	SK-N-SH_RA	brain:	n/a	chr8:8412824-8412838
22	TEAD4	chr8:8412660-8413623	SK-N-SH	brain:	n/a	n/a
23	NFIC	chr8:8412349-8414347	SK-N-SH	brain:	n/a	n/a
24	PBX3	chr8:8412418-8414264	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr8:8412467-8414336	SK-N-SH	brain:	n/a	n/a
26	MAX	chr8:8412775-8413579	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr8:8412613-8413421	A549	lung:	n/a	chr8:8412892-8412902 chr8:8412946-8412957
28	YY1	chr8:8412840-8413559	SK-N-SH	brain:	n/a	chr8:8413328-8413337
29	POLR2A	chr8:8412545-8413455	SK-N-SH	brain:	n/a	n/a
30	ZBTB33	chr8:8412839-8413406	SK-N-SH	brain:	n/a	n/a
31	EP300	chr8:8412562-8413514	SK-N-SH	brain:	n/a	chr8:8412824-8412838
32	FOSL2	chr8:8412681-8413578	SK-N-SH	brain:	n/a	chr8:8413064-8413072 chr8:8413063-8413073
33	GATA3	chr8:8412421-8414340	SK-N-SH	brain:	n/a	chr8:8414020-8414029 chr8:8412584-8412594 chr8:8413610-8413621 chr8:8412892-8412902 chr8:8414025-8414032 chr8:8412946-8412957
34	ZBTB33	chr8:8412791-8413459	SK-N-SH	brain:	n/a	n/a
35	GATA3	chr8:8412358-8414386	SK-N-SH	brain:	n/a	chr8:8414020-8414029 chr8:8412584-8412594 chr8:8413610-8413621 chr8:8412892-8412902 chr8:8414025-8414032 chr8:8412946-8412957
36	RXRA	chr8:8412711-8414264	SK-N-SH	brain:	n/a	n/a
37	FOXM1	chr8:8412770-8413556	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr8:8412769-8413454	SK-N-SH_RA	brain:	n/a	n/a
39	POLR2A	chr8:8412671-8413446	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:8405511..8408091-chr8:8411497..8414103,2	MCF-7	breast:
2	chr8:8411447..8415576-chr8:8419918..8422813,4	MCF-7	breast:
3	chr8:8395182..8397914-chr8:8412349..8414858,2	MCF-7	breast:
4	chr8:8411777..8414467-chr8:8512420..8515459,3	MCF-7	breast:
5	chr8:8242353..8245621-chr8:8412264..8415410,4	MCF-7	breast:
6	chr8:8403320..8405523-chr8:8412097..8413733,2	K562	blood:
7	chr8:8317642..8319537-chr8:8411427..8414292,2	MCF-7	breast:
8	chr8:8411664..8414236-chr8:8423427..8425709,2	MCF-7	breast:
9	chr8:8412630..8415274-chr8:8423101..8424700,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRAGMIN.1-4	chr8:8413248-8413598	ENSG00000253343

Variant related genes	Relation type
ENSG00000253774	TF binding region
ENSG00000254153	Chromatin interaction
ENSG00000182319	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10086615	0.86[ASN][1000 genomes]
rs10108910	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11781563	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11993942	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12550186	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13272989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001445	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28611351	0.95[ASN][1000 genomes]
rs34450143	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34747700	0.85[ASN][1000 genomes]
rs35491016	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35990411	0.90[ASN][1000 genomes]
rs3748145	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3748146	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4295668	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4398919	0.97[ASN][1000 genomes]
rs4418341	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4448277	0.94[ASN][1000 genomes]
rs4567044	0.94[ASN][1000 genomes]
rs55892734	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56738524	0.89[ASN][1000 genomes]
rs6601710	0.84[ASN][1000 genomes]
rs7002609	0.97[ASN][1000 genomes]
rs7005440	0.84[EUR][1000 genomes]
rs7016037	0.96[ASN][1000 genomes]
rs7820527	0.83[ASN][1000 genomes]
rs7833246	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv465452	chr8:8313010-8450761	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv610173	chr8:8313010-8450761	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv465453	chr8:8318850-8439068	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv610174	chr8:8318850-8439068	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv470182	chr8:8318850-8448429	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv465454	chr8:8318850-8448688	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv465455	chr8:8318850-8448688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv610175	chr8:8318850-8448688	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv465456	chr8:8318850-8450761	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv465457	chr8:8318850-8450761	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv610176	chr8:8318850-8450761	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv610177	chr8:8318850-8454531	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv1026251	chr8:8319925-8448688	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv1025433	chr8:8324419-8432339	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1020159	chr8:8324419-8450231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv539455	chr8:8324419-8450231	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	nsv890333	chr8:8328101-8456563	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
27	nsv890334	chr8:8328101-8471348	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv465458	chr8:8341105-8415810	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
29	nsv610178	chr8:8341105-8415810	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
30	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
31	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
32	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
33	nsv890335	chr8:8394297-8448429	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
34	nsv890336	chr8:8396676-8500562	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2294143	FAM167A	cis	parietal	SCAN
rs2294143	SGK223	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8403600-8421400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:8406400-8413600	Enhancers	NHLF	lung
3	chr8:8406400-8414200	Weak transcription	Stomach Mucosa	stomach
4	chr8:8406400-8414800	Enhancers	NHDF-Ad	bronchial
5	chr8:8408800-8413800	Weak transcription	HUVEC	blood vessel
6	chr8:8408800-8414200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:8408800-8414200	Weak transcription	Spleen	Spleen
8	chr8:8410800-8414600	Weak transcription	Fetal Lung	lung
9	chr8:8411800-8414400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr8:8412000-8413400	Enhancers	Ovary	ovary
11	chr8:8412000-8413600	Enhancers	Left Ventricle	heart
12	chr8:8412000-8414800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:8412200-8413800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:8412200-8414000	Enhancers	NHEK	skin
15	chr8:8412200-8414400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:8412400-8413800	Enhancers	HSMM	muscle
17	chr8:8412400-8413800	Enhancers	NH-A	brain
18	chr8:8412400-8414000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:8412400-8414800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:8412600-8413600	Enhancers	Hela-S3	cervix
21	chr8:8412600-8413800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:8412600-8414000	Enhancers	HMEC	breast
23	chr8:8412600-8414800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:8412600-8414800	Enhancers	A549	lung
25	chr8:8412800-8413400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:8412800-8413600	Bivalent Enhancer	Adipose Nuclei	Adipose
27	chr8:8412800-8413600	Enhancers	HSMMtube	muscle
28	chr8:8412800-8413800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:8413000-8414600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr8:8413200-8413400	Flanking Active TSS	Osteobl	bone
31	chr8:8413200-8413600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:8413200-8413600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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