Variant report

Variant	rs11980902
Chromosome Location	chr7:101448046-101448047
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101331341..101332151-chr7:101448037..101448804,2	MCF-7	breast:
2	chr7:101446075..101448443-chr7:101452327..101453917,2	K562	blood:
3	chr7:101446704..101449340-chr7:101499387..101502375,2	K562	blood:
4	chr7:101446447..101448441-chr7:101533510..101536360,2	MCF-7	breast:
5	chr7:101386153..101388465-chr7:101446824..101448422,2	MCF-7	breast:
6	chr7:101437526..101440665-chr7:101445338..101450249,4	K562	blood:
7	chr7:101434891..101437253-chr7:101447491..101449086,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11974028	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55818034	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343746	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57249325	1.00[ASN][1000 genomes]
rs62463713	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv831079	chr7:101273495-101466776	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1021797	chr7:101342353-101466957	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv539046	chr7:101342353-101466957	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv824243	chr7:101445202-101479651	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11980902	PCOLCE	cis	cerebellum	SCAN
rs11980902	MUC17	cis	parietal	SCAN
rs11980902	PVRIG	cis	cerebellum	SCAN
rs11980902	SERPINE1	cis	cerebellum	SCAN
rs11980902	PDAP1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101436800-101457400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:101444800-101448200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr7:101446400-101448400	Enhancers	Placenta	Placenta
4	chr7:101446400-101449400	Bivalent Enhancer	Fetal Intestine Large	intestine
5	chr7:101446600-101448600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr7:101446800-101448400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:101446800-101448800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr7:101446800-101448800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr7:101447000-101448200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr7:101447000-101448200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:101447000-101448200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr7:101447000-101448400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:101447000-101448600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:101447000-101448600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
15	chr7:101447000-101448800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:101447200-101448200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:101447200-101448200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:101447200-101448200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:101447200-101448200	Bivalent Enhancer	Fetal Heart	heart
20	chr7:101447200-101448200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr7:101447200-101448400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr7:101447200-101448400	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr7:101447200-101448400	Enhancers	HMEC	breast
24	chr7:101447200-101448800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr7:101447200-101448800	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr7:101447400-101448200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr7:101447400-101448200	Flanking Bivalent TSS/Enh	NHEK	skin
28	chr7:101447400-101448400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr7:101447400-101448400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:101447400-101448400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
31	chr7:101447400-101448600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr7:101447400-101448600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr7:101447400-101449000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr7:101447600-101448200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr7:101447600-101448200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:101447600-101448400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr7:101447600-101449000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr7:101447800-101448200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
39	chr7:101447800-101449000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr7:101447800-101449800	Enhancers	Fetal Thymus	thymus
41	chr7:101447800-101449800	Enhancers	K562	blood
42	chr7:101448000-101448200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr7:101448000-101448200	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr7:101448000-101448200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:101448000-101448200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
46	chr7:101448000-101448200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
47	chr7:101448000-101448200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
48	chr7:101448000-101448200	Bivalent Enhancer	Rectal Smooth Muscle	rectum
49	chr7:101448000-101448200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
50	chr7:101448000-101448200	Bivalent Enhancer	A549	lung

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