Variant report

Variant	rs7762245
Chromosome Location	chr6:36716229-36716230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36713858..36716285-chr6:36724983..36726678,2	MCF-7	breast:
2	chr6:36714240..36716919-chr6:36719945..36722727,5	MCF-7	breast:
3	chr6:36711266..36713245-chr6:36715954..36717794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13209922	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs3213537	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs55806450	0.86[ASN][1000 genomes]
rs55861143	0.86[ASN][1000 genomes]
rs59030356	0.87[ASN][1000 genomes]
rs7773454	0.84[CHB][hapmap]
rs929052	0.84[CHB][hapmap]
rs929053	0.84[CHB][hapmap]
rs929054	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs929055	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv885809	chr6:36687518-36719079	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv885811	chr6:36695223-36719079	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv885814	chr6:36704807-36722842	Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv602951	chr6:36706157-36719079	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7762245	TULP1	cis	cerebellum	SCAN
rs7762245	MAPK14	cis	parietal	SCAN
rs7762245	LRFN2	cis	cerebellum	SCAN
rs7762245	C11orf65	trans	cerebellum	SCAN
rs7762245	CDKN1A	cis	multi-tissue	Pritchard
rs7762245	CDKN1A	cis	Lymphoblastoid	GTEx
rs7762245		cis	Lymphoblastoid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36703400-36718000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:36703800-36718000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:36704000-36718000	Weak transcription	Right Atrium	heart
4	chr6:36704000-36720400	Weak transcription	Right Ventricle	heart
5	chr6:36708400-36720800	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr6:36709200-36727000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:36711800-36719800	Weak transcription	Gastric	stomach
8	chr6:36712400-36718400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:36712600-36719000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:36713400-36716400	Strong transcription	Primary B cells from cord blood	blood
11	chr6:36713400-36718800	Weak transcription	Colonic Mucosa	Colon
12	chr6:36713600-36717600	Weak transcription	Stomach Mucosa	stomach
13	chr6:36713800-36718000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:36715000-36718200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:36715800-36716800	ZNF genes & repeats	Spleen	Spleen
16	chr6:36716000-36716800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:36716000-36719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:36716200-36717000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:36716200-36717000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
20	chr6:36716200-36717200	ZNF genes & repeats	Fetal Muscle Leg	muscle

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