Variant report

Variant	rs7557904
Chromosome Location	chr2:112931936-112931937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112930506..112933446-chr2:113032238..113034167,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11900153	0.81[CHB][hapmap]
rs12465398	0.81[CHB][hapmap]
rs12711735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13001618	0.81[CHB][hapmap]
rs13031326	0.80[CHB][hapmap]
rs13387246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13394408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13402356	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2312459	0.81[CHB][hapmap]
rs3811643	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4848280	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849050	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591933	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7557904	ZC3H8	cis	parietal	SCAN
rs7557904	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7557904	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112896400-112934600	Weak transcription	Aorta	Aorta
2	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:112918400-112939200	Weak transcription	Gastric	stomach
4	chr2:112918600-112939200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:112919000-112939000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:112919600-112933400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:112919800-112933200	Weak transcription	Thymus	Thymus
8	chr2:112925200-112932800	Weak transcription	Fetal Thymus	thymus
9	chr2:112926000-112937000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:112926400-112932800	Weak transcription	Fetal Stomach	stomach
11	chr2:112926600-112934000	Weak transcription	NHDF-Ad	bronchial
12	chr2:112930800-112934200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:112931000-112932000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:112931200-112932000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:112931200-112932000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:112931200-112932000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:112931200-112932000	Enhancers	Fetal Muscle Leg	muscle
18	chr2:112931200-112932200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr2:112931400-112932000	Flanking Active TSS	HepG2	liver
20	chr2:112931400-112933400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:112931600-112932200	Enhancers	Primary T cells from cord blood	blood
22	chr2:112931600-112932200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:112931600-112933000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:112931800-112932200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:112931800-112933400	Weak transcription	Fetal Lung	lung

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