Variant report

Variant	rs34312198
Chromosome Location	chr7:99674870-99674871
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99672281..99674937-chr7:99777668..99780640,2	K562	blood:
2	chr7:99673231..99675072-chr7:100026135..100027945,2	K562	blood:
3	chr7:99668310..99676246-chr7:99677185..99681836,16	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MCM7-2	chr7:99674641-99675056	NONHSAT122305

Variant related genes	Relation type
ENSG00000166526	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12705074	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs13242458	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34766893	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6955348	1.00[ASW][hapmap];0.85[GIH][hapmap]
rs73156680	1.00[AFR][1000 genomes]
rs73156683	1.00[AFR][1000 genomes]
rs73158413	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34312198	PMPCB	cis	parietal	SCAN
rs34312198	ZSCAN21	cis	parietal	SCAN
rs34312198	TIMP1	trans	lymphoblastoid	seeQTL
rs34312198	ACTL6B	cis	parietal	SCAN
rs34312198	AP4M1	cis	cerebellum	SCAN
rs34312198	PILRB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99661600-99675200	ZNF genes & repeats	A549	lung
2	chr7:99666000-99675000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
3	chr7:99666400-99677200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:99666400-99678000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:99666800-99675200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr7:99666800-99677000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:99667400-99675000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:99667400-99675000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
9	chr7:99667600-99675200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:99669400-99675000	Strong transcription	Brain Angular Gyrus	brain
11	chr7:99669600-99675000	Strong transcription	Brain Cingulate Gyrus	brain
12	chr7:99669600-99675200	Strong transcription	Brain Anterior Caudate	brain
13	chr7:99669600-99677600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:99669800-99675000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr7:99670200-99675000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:99670200-99675200	Strong transcription	Right Ventricle	heart
17	chr7:99670200-99676600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr7:99670400-99675000	Strong transcription	Fetal Brain Male	brain
19	chr7:99670400-99675000	Strong transcription	Gastric	stomach
20	chr7:99670400-99675200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:99670400-99675200	Strong transcription	Rectal Smooth Muscle	rectum
22	chr7:99670400-99676200	Strong transcription	Brain Hippocampus Middle	brain
23	chr7:99670400-99676400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:99670400-99676600	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr7:99670400-99677000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr7:99670600-99675400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:99670600-99675600	Strong transcription	Left Ventricle	heart
28	chr7:99670600-99676000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:99670600-99677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:99670600-99677600	Strong transcription	Primary T cells from cord blood	blood
31	chr7:99670800-99675000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:99670800-99675000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:99670800-99675000	Strong transcription	Adipose Nuclei	Adipose
34	chr7:99670800-99675000	Strong transcription	Colonic Mucosa	Colon
35	chr7:99670800-99675000	Strong transcription	Pancreas	Pancrea
36	chr7:99670800-99675200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:99670800-99675200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:99670800-99675200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr7:99670800-99675200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:99670800-99675200	Strong transcription	HSMMtube	muscle
41	chr7:99670800-99675400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:99670800-99675800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:99670800-99676400	Strong transcription	Dnd41	blood
44	chr7:99670800-99677000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr7:99670800-99677400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:99670800-99677400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:99671000-99675000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:99671000-99675000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:99671000-99676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:99671000-99676600	Weak transcription	Right Atrium	heart

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