Variant report

Variant	rs6946706
Chromosome Location	chr7:100895893-100895894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:288)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:288 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr7:100894999-100896008	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr7:100895298-100895926	H1-hESC	embryonic stem cell:	n/a	n/a
3	IRF1	chr7:100895224-100896063	K562	blood:	n/a	chr7:100895812-100895826 chr7:100895714-100895728 chr7:100895812-100895822 chr7:100895808-100895822
4	GABPA	chr7:100895015-100896035	MCF-7	breast:	n/a	n/a
5	ELF1	chr7:100895172-100895923	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:100895298-100896039	GM15510	blood:	n/a	n/a
7	POLR2A	chr7:100895215-100895951	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:100895697-100895955	HepG2	liver:	n/a	n/a
9	JUND	chr7:100895361-100895987	A549	lung:	n/a	chr7:100895714-100895723
10	SIX5	chr7:100895168-100896093	A549	lung:	n/a	n/a
11	BHLHE40	chr7:100895412-100895912	GM12878	blood:	n/a	n/a
12	TBP	chr7:100895400-100896042	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:100895210-100896044	Hela-S3	cervix:	n/a	n/a
14	ELF1	chr7:100895228-100895945	A549	lung:	n/a	n/a
15	POLR2A	chr7:100895180-100896107	U87	brain:	n/a	n/a
16	POLR2A	chr7:100895320-100896045	HepG2	liver:	n/a	n/a
17	MAZ	chr7:100894966-100896073	IMR90	lung:	n/a	n/a
18	USF1	chr7:100895432-100895898	K562	blood:	n/a	n/a
19	EP300	chr7:100895167-100895952	A549	lung:	n/a	n/a
20	POLR2A	chr7:100895670-100895918	A549	lung:	n/a	n/a
21	RCOR1	chr7:100895509-100895912	Hela-S3	cervix:	n/a	n/a
22	GATA2	chr7:100895472-100896023	SH-SY5Y	brain:	n/a	chr7:100895840-100895847
23	ELF1	chr7:100894917-100896114	MCF-7	breast:	n/a	n/a
24	POLR2A	chr7:100895260-100896106	PANC-1	pancreas:	n/a	n/a
25	ZMIZ1	chr7:100895262-100895986	K562	blood:	n/a	n/a
26	SP1	chr7:100895385-100895943	GM12878	blood:	n/a	chr7:100895714-100895726 chr7:100895711-100895725 chr7:100895715-100895724 chr7:100895733-100895746 chr7:100895716-100895725 chr7:100895714-100895726
27	WRNIP1	chr7:100895239-100895919	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:100895212-100896090	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr7:100895188-100896074	GM12891	blood:	n/a	n/a
30	POLR2A	chr7:100895344-100896022	U87	brain:	n/a	n/a
31	MXI1	chr7:100895145-100896002	GM12878	blood:	n/a	n/a
32	USF1	chr7:100895464-100895986	SK-N-SH_RA	brain:	n/a	n/a
33	ZNF384	chr7:100895481-100895910	K562	blood:	n/a	n/a
34	POLR2A	chr7:100895138-100895945	K562	blood:	n/a	n/a
35	POLR2A	chr7:100895124-100895922	MCF-7	breast:	n/a	n/a
36	ARID3A	chr7:100895540-100895972	HepG2	liver:	n/a	n/a
37	HEY1	chr7:100895749-100895960	HepG2	liver:	n/a	n/a
38	HCFC1	chr7:100895045-100896220	Hela-S3	cervix:	n/a	n/a
39	HEY1	chr7:100895238-100896062	HepG2	liver:	n/a	n/a
40	TRIM28	chr7:100895146-100896072	K562	blood:	n/a	n/a
41	TAF1	chr7:100895237-100896114	ECC-1	luminal epithelium:	n/a	n/a
42	GABPA	chr7:100895354-100895906	K562	blood:	n/a	n/a
43	NFIC	chr7:100895220-100895953	GM12878	blood:	n/a	n/a
44	TAF1	chr7:100895328-100895973	SK-N-SH	brain:	n/a	n/a
45	SP2	chr7:100895092-100895939	HepG2	liver:	n/a	n/a
46	JUN	chr7:100894703-100896208	K562	blood:	n/a	chr7:100895714-100895723
47	USF2	chr7:100895558-100895925	HepG2	liver:	n/a	n/a
48	POLR2A	chr7:100895326-100896055	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:100895247-100896010	NB4	blood:	n/a	n/a
50	TAF1	chr7:100895308-100896040	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100858946..100862708-chr7:100892771..100897292,5	MCF-7	breast:
2	chr7:100859477..100861456-chr7:100895747..100897273,2	K562	blood:
3	chr7:100859404..100861068-chr7:100894037..100896793,2	MCF-7	breast:
4	chr7:100807181..100809007-chr7:100895372..100897071,2	K562	blood:
5	chr7:100881101..100885645-chr7:100894081..100896862,4	MCF-7	breast:
6	chr7:100728621..100730334-chr7:100895129..100897710,2	MCF-7	breast:
7	chr7:100486731..100489034-chr7:100894336..100897176,2	MCF-7	breast:
8	chr7:100806299..100808867-chr7:100894642..100897117,2	MCF-7	breast:
9	chr7:100860572..100862632-chr7:100892717..100896862,3	K562	blood:

No data

Variant related genes	Relation type
FIS1	TF binding region
ENSG00000176125	Chromatin interaction
ENSG00000214253	Chromatin interaction
ENSG00000106404	Chromatin interaction
ENSG00000106400	Chromatin interaction
ENSG00000106397	Chromatin interaction
ENSG00000169871	Chromatin interaction
ENSG00000128564	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10215699	0.95[EUR][1000 genomes]
rs10230349	0.87[AMR][1000 genomes]
rs10230367	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10241107	0.95[EUR][1000 genomes]
rs10244139	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10252307	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10252506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10257072	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10260707	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10260813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10270498	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10273837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10487887	0.95[EUR][1000 genomes]
rs12333955	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12334190	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28535695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28582264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28629340	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28673822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28689891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56099342	0.82[AFR][1000 genomes]
rs56212758	0.82[AFR][1000 genomes]
rs56749963	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57295609	0.82[AFR][1000 genomes]
rs57422827	0.81[AFR][1000 genomes]
rs58341321	0.81[AFR][1000 genomes]
rs59554944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59619028	0.82[AFR][1000 genomes]
rs59937851	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60536711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60719606	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60774938	0.81[AFR][1000 genomes]
rs61069336	0.81[AFR][1000 genomes]
rs6946705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6957526	0.95[EUR][1000 genomes]
rs6961873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6964812	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6967483	0.95[EUR][1000 genomes]
rs6975417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979122	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979308	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979710	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73713820	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73713821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73713822	0.93[AFR][1000 genomes]
rs73713824	0.81[AFR][1000 genomes]
rs73713827	0.81[AFR][1000 genomes]
rs7778271	0.91[EUR][1000 genomes]
rs7808669	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv534186	chr7:100773842-100898909	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv464651	chr7:100792810-100971604	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv607974	chr7:100792810-100971604	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	54 gene(s)	inside rSNPs	diseases
9	esv2752134	chr7:100800131-101141867	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv831076	chr7:100828847-101011674	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv888819	chr7:100833153-100920007	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv2422326	chr7:100833449-101000131	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
13	nsv607978	chr7:100861213-100971604	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
14	nsv831077	chr7:100874209-101083930	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6946706	CLDN15	cis	Whole Blood	GTEx
rs6946706	FIS1	cis	Artery Tibial	GTEx
rs6946706	CLDN15	cis	Esophagus Muscularis	GTEx
rs6946706	CLDN15	cis	Skin Sun Exposed Lower leg	GTEx
rs6946706	FIS1	cis	Thyroid	GTEx
rs6946706	FIS1	Cis_1M	lymphoblastoid	RTeQTL
rs6946706	CLDN15	cis	multi-tissue	Pritchard
rs6946706	FIS1	cis	Adipose Subcutaneous	GTEx
rs6946706	FIS1	cis	Stomach	GTEx
rs6946706	FIS1	cis	Heart Left Ventricle	GTEx
rs6946706	FIS1	cis	lung	GTEx
rs6946706	CLDN15	Cis_1M	lymphoblastoid	RTeQTL
rs6946706	FIS1	cis	Skin Sun Exposed Lower leg	GTEx
rs6946706	FIS1	cis	Artery Aorta	GTEx
rs6946706	FIS1	cis	Esophagus Mucosa	GTEx
rs6946706	FIS1	cis	Esophagus Muscularis	GTEx
rs6946706	FIS1	cis	Whole Blood	GTEx
rs6946706	CLDN15	cis	Thyroid	GTEx
rs6946706	CLDN15	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100894000-100896200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:100894000-100896400	Active TSS	K562	blood
3	chr7:100894400-100896200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:100894400-100896200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:100894400-100896200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:100894400-100896200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr7:100894400-100896200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr7:100894400-100896200	Active TSS	HSMM	muscle
9	chr7:100894400-100896400	Active TSS	A549	lung
10	chr7:100894600-100896000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr7:100894600-100896000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:100894600-100896200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr7:100894600-100896200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr7:100894600-100896400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:100894800-100896000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:100894800-100896000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:100894800-100896000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:100894800-100896000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:100894800-100896000	Active TSS	Esophagus	oesophagus
20	chr7:100894800-100896000	Active TSS	Gastric	stomach
21	chr7:100894800-100896000	Active TSS	HSMMtube	muscle
22	chr7:100894800-100896200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:100894800-100896200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr7:100894800-100896200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr7:100894800-100896200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr7:100894800-100896200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:100894800-100896200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:100894800-100896200	Active TSS	Muscle Satellite Cultured Cells	--
29	chr7:100894800-100896200	Active TSS	Fetal Intestine Small	intestine
30	chr7:100894800-100896200	Active TSS	Fetal Kidney	kidney
31	chr7:100894800-100896200	Active TSS	Small Intestine	intestine
32	chr7:100894800-100896200	Active TSS	Hela-S3	cervix
33	chr7:100894800-100896200	Active TSS	HMEC	breast
34	chr7:100894800-100896200	Active TSS	NH-A	brain
35	chr7:100894800-100896200	Active TSS	NHLF	lung
36	chr7:100894800-100896200	Active TSS	Osteobl	bone
37	chr7:100894800-100896400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr7:100894800-100896400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr7:100894800-100896400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:100894800-100896400	Active TSS	Brain Substantia Nigra	brain
41	chr7:100894800-100896400	Active TSS	Colonic Mucosa	Colon
42	chr7:100894800-100896400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr7:100894800-100896400	Active TSS	Fetal Intestine Large	intestine
44	chr7:100894800-100896400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr7:100894800-100896400	Active TSS	GM12878-XiMat	blood
46	chr7:100894800-100896400	Active TSS	NHDF-Ad	bronchial
47	chr7:100895000-100896000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:100895000-100896000	Active TSS	Lung	lung
49	chr7:100895000-100896000	Active TSS	Placenta Amnion	Placenta Amnion
50	chr7:100895000-100896000	Active TSS	Sigmoid Colon	Sigmoid Colon

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