Variant report

Variant	rs4948104
Chromosome Location	chr7:56142519-56142520
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	POLR2A	chr7:56142032-56142534	MCF10A-Er-Src	breast:	n/a	n/a
2	ELF1	chr7:56142017-56142557	MCF-7	breast:	n/a	chr7:56142243-56142252
3	POLR2A	chr7:56141973-56142521	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr7:56141869-56142546	GM12892	blood:	n/a	n/a
5	EP300	chr7:56142017-56142532	T-47D	breast:	n/a	n/a
6	ZMIZ1	chr7:56141883-56142673	K562	blood:	n/a	n/a
7	MAX	chr7:56142068-56142559	MCF-7	breast:	n/a	n/a
8	CTCF	chr7:56141960-56142571	IMR90	lung:	n/a	chr7:56142175-56142193 chr7:56142177-56142190 chr7:56142180-56142188 chr7:56142176-56142192 chr7:56142170-56142191
9	RAD21	chr7:56141747-56142550	HCT-116	colon:	n/a	chr7:56142173-56142192 chr7:56142183-56142190
10	NFIC	chr7:56141973-56142564	ECC-1	luminal epithelium:	n/a	n/a
11	ELF1	chr7:56141986-56142608	GM12878	blood:	n/a	chr7:56142243-56142252
12	CHD1	chr7:56141897-56142587	IMR90	lung:	n/a	n/a
13	PBX3	chr7:56141830-56142545	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr7:56141616-56142626	A549	lung:	n/a	chr7:56142175-56142193 chr7:56142177-56142190 chr7:56142180-56142188 chr7:56142176-56142192 chr7:56142170-56142191
15	MXI1	chr7:56141701-56142716	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr7:56141750-56142543	HCT-116	colon:	n/a	chr7:56142175-56142193 chr7:56142177-56142190 chr7:56142180-56142188 chr7:56142176-56142192 chr7:56142170-56142191
17	MAX	chr7:56142055-56142573	ECC-1	luminal epithelium:	n/a	n/a
18	SMC3	chr7:56141595-56142629	SK-N-SH	brain:	n/a	chr7:56142177-56142191
19	CTCF	chr7:56141513-56142835	SK-N-SH	brain:	n/a	chr7:56142175-56142193 chr7:56142177-56142190 chr7:56142180-56142188 chr7:56142176-56142192 chr7:56142170-56142191
20	POLR2A	chr7:56141761-56142599	SK-N-MC	brain:	n/a	n/a
21	CTCF	chr7:56142460-56142610	A549	lung:	n/a	n/a
22	POLR2A	chr7:56142505-56142527	K562	blood:	n/a	n/a
23	RAD21	chr7:56141613-56142687	SK-N-SH	brain:	n/a	chr7:56142173-56142192 chr7:56142183-56142190
24	CTCF	chr7:56142470-56142521	GM10266	blood:	n/a	n/a
25	HA-E2F1	chr7:56141977-56142613	MCF-7	breast:	n/a	n/a
26	POLR2A	chr7:56140513-56143098	K562	blood:	n/a	n/a
27	POLR2A	chr7:56142011-56142545	K562	blood:	n/a	n/a
28	RAD21	chr7:56141814-56142571	IMR90	lung:	n/a	chr7:56142173-56142192 chr7:56142183-56142190
29	POLR2A	chr7:56142003-56142909	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:56119174..56121015-chr7:56139907..56143557,3	MCF-7	breast:
2	chr7:56131320..56133312-chr7:56141582..56144695,3	MCF-7	breast:
3	chr7:56031249..56033824-chr7:56141998..56144238,2	MCF-7	breast:
4	chr7:56140520..56143096-chr7:56151808..56154646,2	K562	blood:
5	chr7:56072282..56073173-chr7:56141696..56142725,3	K562	blood:
6	chr7:56130207..56133425-chr7:56142360..56145052,4	K562	blood:

Variant related genes	Relation type
SUMF2	TF binding region
ENSG00000129103	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10081373	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10255049	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11238389	0.84[ASN][1000 genomes]
rs11771788	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537943	0.91[ASN][1000 genomes]
rs12669623	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240915	0.88[ASN][1000 genomes]
rs13241866	0.88[ASN][1000 genomes]
rs13244654	0.95[ASN][1000 genomes]
rs2002651	0.94[ASN][1000 genomes]
rs2016724	0.92[ASN][1000 genomes]
rs2230197	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242508	0.93[ASN][1000 genomes]
rs2538047	0.89[ASN][1000 genomes]
rs3735665	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4049337	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4275190	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947534	0.81[ASN][1000 genomes]
rs4948102	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62457261	0.80[ASN][1000 genomes]
rs6593297	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6954546	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6955423	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6958480	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966609	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6973917	0.82[ASN][1000 genomes]
rs6975311	0.82[ASN][1000 genomes]
rs766333	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776550	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7793921	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7801467	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811270	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811755	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9767946	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats 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 target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4948104	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56132400-56145400	Weak transcription	Spleen	Spleen
3	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
6	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
7	chr7:56133400-56144200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:56133600-56144200	Weak transcription	NHDF-Ad	bronchial
10	chr7:56133600-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:56133800-56143200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
15	chr7:56135000-56142600	Strong transcription	Fetal Stomach	stomach
16	chr7:56137200-56146000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:56138200-56144200	Weak transcription	Hela-S3	cervix
18	chr7:56138600-56144200	Weak transcription	Fetal Lung	lung
19	chr7:56138600-56144200	Weak transcription	Right Ventricle	heart
20	chr7:56138800-56146800	Weak transcription	Aorta	Aorta
21	chr7:56138800-56146800	Weak transcription	HSMMtube	muscle
22	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:56139000-56144000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:56139000-56144200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr7:56139000-56144200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:56139000-56144200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:56139000-56144200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:56139000-56144200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr7:56139000-56144200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:56139000-56144200	Weak transcription	A549	lung
32	chr7:56139000-56144200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr7:56139000-56144400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr7:56139000-56145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:56139000-56145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:56139000-56145600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:56139000-56146800	Weak transcription	HSMM	muscle
38	chr7:56139000-56147000	Weak transcription	NH-A	brain
39	chr7:56139200-56144200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:56139200-56146400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:56139400-56144200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:56139400-56144400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:56139400-56144400	Weak transcription	Lung	lung
44	chr7:56139400-56146000	Weak transcription	Primary B cells from cord blood	blood
45	chr7:56139400-56146000	Weak transcription	Brain Angular Gyrus	brain
46	chr7:56140200-56142800	Strong transcription	Fetal Thymus	thymus
47	chr7:56140400-56143000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:56140400-56152000	Strong transcription	Dnd41	blood
49	chr7:56140600-56142600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:56140800-56153000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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