Variant report

Variant	rs2227272
Chromosome Location	chr7:108209623-108209624
allele	C/T
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	POLR2A	chr7:108209465-108210794	Hela-S3	cervix:	n/a	n/a
2	BRCA1	chr7:108209621-108210666	GM12878	blood:	n/a	n/a
3	MAX	chr7:108209409-108210831	A549	lung:	n/a	chr7:108209636-108209645
4	MAX	chr7:108209449-108211215	Hela-S3	cervix:	n/a	chr7:108209636-108209645
5	ELF1	chr7:108209617-108210933	GM12878	blood:	n/a	chr7:108209945-108209958
6	E2F6	chr7:108209399-108210973	H1-hESC	embryonic stem cell:	n/a	chr7:108210790-108210800
7	E2F4	chr7:108209187-108210522	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr7:108209607-108210915	GM12878	blood:	n/a	n/a
9	FOXM1	chr7:108209441-108210606	GM12878	blood:	n/a	n/a
10	TAF1	chr7:108209581-108210570	A549	lung:	n/a	n/a
11	TAF1	chr7:108209515-108210728	ECC-1	luminal epithelium:	n/a	n/a
12	MBD4	chr7:108209529-108210546	HepG2	liver:	n/a	n/a
13	POLR2A	chr7:108209545-108210728	U87	brain:	n/a	n/a
14	MYC	chr7:108209506-108210668	K562	blood:	n/a	chr7:108209636-108209645
15	MYC	chr7:108209471-108211384	K562	blood:	n/a	chr7:108209636-108209645
16	NFATC1	chr7:108209300-108210246	GM12878	blood:	n/a	n/a
17	RFX5	chr7:108209598-108209746	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr7:108209066-108211445	GM12891	blood:	n/a	n/a
19	CEBPB	chr7:108209493-108209709	K562	blood:	n/a	n/a
20	MYC	chr7:108209467-108211334	NB4	blood:	n/a	chr7:108209636-108209645
21	POLR2A	chr7:108209567-108210815	PFSK-1	brain:	n/a	n/a
22	MAX	chr7:108209197-108211617	K562	blood:	n/a	chr7:108209636-108209645
23	POLR2A	chr7:108208976-108212142	MCF10A-Er-Src	breast:	n/a	n/a
24	JUN	chr7:108208251-108211889	K562	blood:	n/a	n/a
25	SIX5	chr7:108209236-108210404	A549	lung:	n/a	n/a
26	POLR2A	chr7:108208967-108210802	SK-N-MC	brain:	n/a	n/a
27	MAX	chr7:108209623-108210575	K562	blood:	n/a	chr7:108209636-108209645
28	HA-E2F1	chr7:108209464-108211305	MCF-7	breast:	n/a	chr7:108210790-108210800
29	POLR2A	chr7:108209575-108210665	GM12878	blood:	n/a	n/a
30	RAD21	chr7:108209453-108210568	H1-hESC	embryonic stem cell:	n/a	n/a
31	TRIM28	chr7:108209462-108211419	K562	blood:	n/a	n/a
32	USF1	chr7:108209370-108210643	K562	blood:	n/a	chr7:108209635-108209646 chr7:108209635-108209648 chr7:108210265-108210276
33	HCFC1	chr7:108209080-108211919	Hela-S3	cervix:	n/a	n/a
34	USF1	chr7:108209474-108209797	SK-N-SH_RA	brain:	n/a	chr7:108209635-108209646 chr7:108209635-108209648
35	MAX	chr7:108209425-108210845	ECC-1	luminal epithelium:	n/a	chr7:108209636-108209645
36	MYC	chr7:108209555-108209645	MCF10A-Er-Src	breast:	n/a	chr7:108209636-108209645
37	POLR2A	chr7:108209614-108211298	H1-neurons	neurons:	n/a	n/a
38	TCF12	chr7:108209257-108210904	A549	lung:	n/a	n/a
39	TAF1	chr7:108209586-108210742	MCF-7	breast:	n/a	n/a
40	MAX	chr7:108209352-108211322	MCF-7	breast:	n/a	chr7:108209636-108209645
41	E2F6	chr7:108209531-108210765	Hela-S3	cervix:	n/a	n/a
42	USF1	chr7:108209408-108210704	ECC-1	luminal epithelium:	n/a	chr7:108209635-108209646 chr7:108209635-108209648 chr7:108210265-108210276
43	E2F6	chr7:108209420-108210902	A549	lung:	n/a	chr7:108210790-108210800
44	POLR2A	chr7:108209604-108211137	GM12878	blood:	n/a	n/a
45	SIN3AK20	chr7:108209623-108211258	SK-N-SH	brain:	n/a	n/a
46	CEBPD	chr7:108209479-108210674	K562	blood:	n/a	n/a
47	CREB1	chr7:108209350-108211351	K562	blood:	n/a	n/a
48	NFIC	chr7:108209185-108210550	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:108209529-108211203	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr7:108209605-108210830	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:88991033..88991701-chr7:108209613..108210220,2	Hela-S3	cervix:
2	chr7:108164038..108167949-chr7:108208349..108211666,8	MCF-7	breast:
3	chr7:107383523..107385849-chr7:108208781..108210517,2	K562	blood:
4	chr17:56735024..56736952-chr7:108209393..108212263,2	MCF-7	breast:
5	chr7:108209606..108210312-chr9:130213295..130213863,2	Hela-S3	cervix:
6	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:
7	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
8	chr7:108208069..108211100-chr7:112089167..112092388,3	K562	blood:
9	chr1:45987399..45988001-chr7:108209389..108210290,2	NB4	blood:
10	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:
11	chr7:108209600..108213665-chr7:112090307..112092525,3	K562	blood:

Variant related genes	Relation type
DNAJB9	TF binding region
ENSG00000135241	Chromatin interaction
ENSG00000153574	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000105879	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000241764	Chromatin interaction
ENSG00000148356	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10215124	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10258344	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155881	0.81[ASW][hapmap];0.82[LWK][hapmap]
rs2041002	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2108254	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2190403	0.90[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2190404	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2214911	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240449	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28667688	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2227272	SLC26A3	cis	parietal	SCAN
rs2227272	DNAJB9	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108207400-108213400	Active TSS	GM12878-XiMat	blood
2	chr7:108207600-108212000	Active TSS	K562	blood
3	chr7:108208400-108209800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr7:108208400-108209800	Active TSS	Stomach Smooth Muscle	stomach
5	chr7:108208400-108211400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:108208400-108211800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:108208400-108212000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:108208600-108211200	Active TSS	Brain Germinal Matrix	brain
9	chr7:108208600-108211400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr7:108208600-108211400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:108208600-108211600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr7:108208600-108211800	Active TSS	NHDF-Ad	bronchial
13	chr7:108208600-108211800	Active TSS	NHLF	lung
14	chr7:108208600-108212000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr7:108208600-108212400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr7:108208800-108209800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:108208800-108209800	Active TSS	HepG2	liver
18	chr7:108208800-108210000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr7:108208800-108211200	Active TSS	Muscle Satellite Cultured Cells	--
20	chr7:108208800-108211200	Active TSS	Brain Cingulate Gyrus	brain
21	chr7:108208800-108211400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:108208800-108211400	Active TSS	Pancreas	Pancrea
23	chr7:108208800-108211600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr7:108208800-108211600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:108208800-108211600	Active TSS	HSMM	muscle
26	chr7:108208800-108211800	Active TSS	H1 Cell Line	embryonic stem cell
27	chr7:108208800-108211800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:108208800-108211800	Active TSS	Placenta	Placenta
29	chr7:108208800-108212200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:108208800-108212200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:108208800-108212400	Active TSS	Right Ventricle	heart
32	chr7:108209000-108209800	Flanking Active TSS	Fetal Brain Female	brain
33	chr7:108209000-108209800	Flanking Active TSS	Fetal Thymus	thymus
34	chr7:108209000-108209800	Flanking Active TSS	HUVEC	blood vessel
35	chr7:108209000-108210000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:108209000-108210000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:108209000-108210000	Active TSS	Right Atrium	heart
38	chr7:108209000-108211200	Active TSS	Brain Substantia Nigra	brain
39	chr7:108209000-108211200	Active TSS	NHEK	skin
40	chr7:108209000-108211400	Active TSS	Placenta Amnion	Placenta Amnion
41	chr7:108209000-108211400	Active TSS	A549	lung
42	chr7:108209000-108211600	Active TSS	Liver	Liver
43	chr7:108209000-108211600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:108209000-108211600	Active TSS	HSMMtube	muscle
45	chr7:108209000-108211800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:108209000-108211800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:108209000-108211800	Active TSS	Fetal Kidney	kidney
48	chr7:108209200-108209800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr7:108209200-108209800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr7:108209200-108210000	Flanking Active TSS	Primary hematopoietic stem cells	blood

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