Variant report

Variant	rs13245629
Chromosome Location	chr7:128020371-128020372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128001106..128003195-chr7:128020192..128022783,2	MCF-7	breast:
2	chr7:127988066..127990303-chr7:128019597..128021947,2	MCF-7	breast:
3	chr7:128014128..128016101-chr7:128018729..128021356,2	K562	blood:

Variant related genes	Relation type
ENSG00000224940	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10251597	1.00[JPT][hapmap]
rs11770116	0.86[CHD][hapmap]
rs11980741	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12672625	1.00[JPT][hapmap]
rs1560214	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2288548	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2288549	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2562730	1.00[JPT][hapmap]
rs2562733	1.00[JPT][hapmap]
rs2562737	1.00[JPT][hapmap]
rs2562740	1.00[JPT][hapmap]
rs2732394	1.00[JPT][hapmap]
rs2732429	1.00[JPT][hapmap]
rs4728108	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4731448	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4731453	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4731454	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6956656	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs880084	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv889191	chr7:127973133-128073326	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv608400	chr7:127978820-128048194	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	esv2493565	chr7:127985695-128053377	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3478325	chr7:127986726-128053483	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3478326	chr7:127986726-128053483	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13245629	CPA1	cis	parietal	SCAN
rs13245629	TMEM209	cis	parietal	SCAN
rs13245629	ATP6V1F	cis	parietal	SCAN
rs13245629	IMPDH1	cis	cerebellum	SCAN
rs13245629	ZNF800	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128002400-128044400	Weak transcription	Right Atrium	heart
2	chr7:128006800-128023400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:128018400-128024400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:128018600-128025000	Enhancers	Fetal Muscle Leg	muscle
5	chr7:128018800-128021800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:128018800-128024600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr7:128019000-128020600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:128019000-128021400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:128019000-128021400	Weak transcription	A549	lung
10	chr7:128019000-128023400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:128019000-128024600	Enhancers	Fetal Muscle Trunk	muscle
12	chr7:128019200-128020600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:128019200-128020600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:128019200-128020800	Enhancers	Psoas Muscle	Psoas
15	chr7:128019200-128024200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:128019200-128024600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:128019400-128024600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:128019600-128021000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:128019600-128022400	Enhancers	HSMMtube	muscle
20	chr7:128019800-128021000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:128020000-128020400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr7:128020000-128021400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr7:128020000-128022400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:128020000-128023200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr7:128020000-128024200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:128020000-128025200	Enhancers	Fetal Thymus	thymus
27	chr7:128020200-128020400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr7:128020200-128021200	Enhancers	Thymus	Thymus

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