Variant report

Variant	rs11978096
Chromosome Location	chr7:100156438-100156439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100154874..100158507-chr7:100159713..100161365,3	K562	blood:
2	chr7:100025919..100028259-chr7:100156062..100159028,2	K562	blood:
3	chr7:100071827..100074750-chr7:100153997..100156937,2	K562	blood:
4	chr7:100141487..100144211-chr7:100154594..100158320,3	MCF-7	breast:
5	chr7:100156209..100158996-chr7:100200461..100203362,3	K562	blood:
6	chr7:100156035..100158297-chr7:100168691..100170406,2	MCF-7	breast:
7	chr7:100156184..100160431-chr7:100180126..100184186,4	MCF-7	breast:
8	chr7:100136557..100138359-chr7:100155320..100157667,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146834	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000106351	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000106336	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11972116	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11977607	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978967	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154919	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406243	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307653	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58509206	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60668677	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743967	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61309832	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61318457	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67147615	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67535650	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154884	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154887	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154891	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154895	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154902	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156207	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156210	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711133	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711136	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711137	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784759	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799695	0.88[AMR][1000 genomes];1.00[EUR][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	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
3	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
4	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
5	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
6	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
8	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11978096	SAP25	cis	Artery Tibial	GTEx
rs11978096	SAP25	cis	Nerve Tibial	GTEx
rs11978096	SAP25	cis	Esophagus Muscularis	GTEx
rs11978096	SAP25	cis	Thyroid	GTEx
rs11978096	SERPINE1	cis	lymphoblastoid	seeQTL
rs11978096	LRCH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100144200-100167000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:100145200-100167400	Weak transcription	HSMM	muscle
3	chr7:100145600-100157000	Weak transcription	Fetal Brain Male	brain
4	chr7:100145800-100157600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:100146200-100165000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:100146400-100157400	Strong transcription	Fetal Stomach	stomach
7	chr7:100146600-100167200	Weak transcription	Fetal Heart	heart
8	chr7:100147000-100157200	Weak transcription	Stomach Mucosa	stomach
9	chr7:100147000-100157400	Weak transcription	Right Atrium	heart
10	chr7:100148600-100157200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:100148600-100160400	Weak transcription	Fetal Lung	lung
12	chr7:100148600-100161800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:100148600-100165000	Weak transcription	Primary B cells from cord blood	blood
14	chr7:100148800-100156800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:100149200-100157000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr7:100149800-100157000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:100150000-100157200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:100150000-100157800	Genic enhancers	HepG2	liver
19	chr7:100150600-100159200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:100150800-100157400	Weak transcription	Fetal Kidney	kidney
21	chr7:100151400-100161400	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:100151400-100167400	Weak transcription	Psoas Muscle	Psoas
23	chr7:100151800-100156800	Weak transcription	Hela-S3	cervix
24	chr7:100152000-100160400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:100152000-100160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr7:100152000-100164600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:100152000-100165600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:100152000-100166000	Weak transcription	NHEK	skin
29	chr7:100152600-100156800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr7:100153400-100157000	Strong transcription	Fetal Intestine Large	intestine
31	chr7:100153600-100157200	Strong transcription	Fetal Intestine Small	intestine
32	chr7:100153600-100160800	Weak transcription	NHLF	lung
33	chr7:100153600-100165000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:100153800-100159200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:100154000-100164600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:100154000-100166800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:100154200-100157000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:100154200-100161800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:100154400-100156600	Weak transcription	Brain Angular Gyrus	brain
40	chr7:100154400-100156600	Weak transcription	Esophagus	oesophagus
41	chr7:100154400-100156600	Weak transcription	Fetal Thymus	thymus
42	chr7:100154400-100156600	Weak transcription	Gastric	stomach
43	chr7:100154400-100156800	Weak transcription	Pancreas	Pancrea
44	chr7:100154400-100157200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr7:100154400-100157200	Weak transcription	Brain Anterior Caudate	brain
46	chr7:100154400-100157200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:100154400-100157400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:100154400-100157400	Weak transcription	Brain Germinal Matrix	brain
49	chr7:100154400-100157400	Weak transcription	Placenta	Placenta
50	chr7:100154400-100159200	Weak transcription	Fetal Brain Female	brain

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