Variant report

Variant	rs73156208
Chromosome Location	chr7:100178552-100178553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100177958-100178693	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr7:100178398-100178895	K562	blood:	n/a	n/a
3	POLR2A	chr7:100177235-100180963	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:100178259-100178673	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:100177965-100178627	GM12891	blood:	n/a	n/a
6	POLR2A	chr7:100178082-100178570	K562	blood:	n/a	n/a
7	POLR2A	chr7:100177981-100178629	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:100178357-100178727	GM12878	blood:	n/a	n/a
9	SUZ12	chr7:100178153-100178604	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr7:100177958-100178772	K562	blood:	n/a	n/a
11	POLR2A	chr7:100177892-100178817	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:100177201-100179008	GM12878	blood:	n/a	n/a
13	NR2C2	chr7:100178204-100178637	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:100178130-100178643	GM12891	blood:	n/a	n/a
15	MAX	chr7:100178391-100178569	NB4	blood:	n/a	chr7:100178457-100178467

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100176059..100178977-chr7:100238614..100240388,2	K562	blood:
2	chr7:100178369..100186125-chr7:100269651..100278553,26	MCF-7	breast:
3	chr7:100059236..100061028-chr7:100176403..100178856,2	K562	blood:

No data

Variant related genes	Relation type
LRCH4	TF binding region
FBXO24	TF binding region
ENSG00000264758	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000172354	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11972116	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11977607	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978096	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978967	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154919	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216707	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406243	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307653	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58509206	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60668677	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743967	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61309832	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61318457	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67147615	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67535650	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970240	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154884	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154887	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154891	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154894	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154895	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154902	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156207	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156210	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711133	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711136	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711137	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784759	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799695	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
9	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
10	nsv888787	chr7:100161557-100179857	ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
11	nsv888788	chr7:100161557-100186066	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	52 gene(s)	inside rSNPs	diseases
12	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv888789	chr7:100166585-100178915	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
14	nsv5868	chr7:100169998-100214646	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases
15	nsv607932	chr7:100172495-100182691	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
16	esv3380438	chr7:100176116-100180514	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs73156208	SAP25	cis	Artery Tibial	GTEx
rs73156208	LRCH4	cis	Esophagus Muscularis	GTEx
rs73156208	SAP25	cis	Nerve Tibial	GTEx
rs73156208	SAP25	cis	Thyroid	GTEx
rs73156208	SAP25	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100168000-100179800	Weak transcription	Right Atrium	heart
2	chr7:100168600-100179600	Strong transcription	NHLF	lung
3	chr7:100169600-100178600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:100169600-100179000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:100169600-100180000	Strong transcription	Fetal Intestine Small	intestine
6	chr7:100169600-100180200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:100169800-100179400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:100169800-100180000	Strong transcription	Thymus	Thymus
9	chr7:100170000-100181200	Weak transcription	Hela-S3	cervix
10	chr7:100170200-100178600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:100170200-100180200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:100170200-100180200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:100170200-100180800	Strong transcription	Brain Germinal Matrix	brain
14	chr7:100170400-100179400	Strong transcription	Esophagus	oesophagus
15	chr7:100170400-100179600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:100170400-100179800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr7:100170400-100180200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:100170600-100178800	Strong transcription	Colonic Mucosa	Colon
19	chr7:100170600-100179200	Strong transcription	Dnd41	blood
20	chr7:100170600-100179600	Strong transcription	Fetal Thymus	thymus
21	chr7:100170600-100180800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr7:100170800-100178600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr7:100170800-100179400	Strong transcription	Gastric	stomach
24	chr7:100170800-100179800	Strong transcription	Fetal Muscle Leg	muscle
25	chr7:100170800-100179800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr7:100171000-100179600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:100171000-100179800	Strong transcription	Adipose Nuclei	Adipose
28	chr7:100171000-100180200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:100171000-100180600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr7:100171200-100179800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:100171400-100180600	Strong transcription	Fetal Brain Female	brain
32	chr7:100171600-100179400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:100171600-100179600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:100171600-100180000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr7:100171600-100180400	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr7:100171600-100180400	Strong transcription	Brain Substantia Nigra	brain
37	chr7:100171600-100180800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:100171600-100181400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:100171600-100181600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:100171800-100179400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr7:100171800-100179800	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr7:100171800-100180200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr7:100171800-100180200	Strong transcription	Left Ventricle	heart
44	chr7:100171800-100180400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:100172000-100179400	Strong transcription	Spleen	Spleen
46	chr7:100172000-100180000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:100172000-100180400	Strong transcription	Brain Anterior Caudate	brain
48	chr7:100172200-100180200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:100172200-100180800	Strong transcription	Brain Hippocampus Middle	brain
50	chr7:100172400-100179600	Strong transcription	Fetal Intestine Large	intestine

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