Variant report

Variant	rs3752480
Chromosome Location	chr6:36710269-36710270
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36706145..36708888-chr6:36709331..36711123,2	MCF-7	breast:
2	chr6:36671517..36673727-chr6:36709746..36712131,2	K562	blood:
3	chr6:36708140..36710606-chr6:36718569..36720077,2	MCF-7	breast:
4	chr6:36588827..36591407-chr6:36708568..36710825,2	MCF-7	breast:
5	chr6:36658059..36660618-chr6:36709664..36711830,2	MCF-7	breast:
6	chr6:36705988..36708979-chr6:36709402..36712073,2	K562	blood:
7	chr6:36710180..36712510-chr6:36716987..36718768,2	K562	blood:
8	chr6:36708174..36711394-chr6:36720287..36721932,3	MCF-7	breast:
9	chr6:36706791..36710785-chr6:36712838..36716064,4	MCF-7	breast:
10	chr6:36646178..36648267-chr6:36708912..36712169,4	MCF-7	breast:
11	chr6:36708918..36710565-chr6:36712727..36715586,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10807173	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11970008	0.81[ASN][1000 genomes]
rs41272176	0.84[AFR][1000 genomes]
rs9368958	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380593	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380594	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv885810	chr6:36695223-36714491	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv520755	chr6:36702284-36713720	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv885813	chr6:36702843-36713720	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv525168	chr6:36704787-36713720	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	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
14	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3752480	ZNF76	cis	cerebellum	SCAN
rs3752480	FANCE	cis	parietal	SCAN
rs3752480	SRSF3	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr6:36703800-36711400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:36703800-36712800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:36703800-36718000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:36704000-36711600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:36704000-36711800	Weak transcription	Brain Anterior Caudate	brain
7	chr6:36704000-36712600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:36704000-36718000	Weak transcription	Right Atrium	heart
9	chr6:36704000-36720400	Weak transcription	Right Ventricle	heart
10	chr6:36704200-36711800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:36707600-36710800	Weak transcription	Gastric	stomach
12	chr6:36707600-36712600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr6:36707800-36711200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:36707800-36711200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:36708000-36711200	Enhancers	Colonic Mucosa	Colon
16	chr6:36708200-36711000	Weak transcription	NHLF	lung
17	chr6:36708400-36720800	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr6:36708800-36710600	Enhancers	Fetal Intestine Small	intestine
19	chr6:36709000-36712800	Enhancers	Fetal Intestine Large	intestine
20	chr6:36709200-36711800	Weak transcription	Spleen	Spleen
21	chr6:36709200-36714800	Enhancers	Esophagus	oesophagus
22	chr6:36709200-36727000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:36709400-36710800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr6:36709400-36711600	Weak transcription	HUVEC	blood vessel
25	chr6:36709600-36710600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:36709600-36711400	Genic enhancers	Primary B cells from cord blood	blood
27	chr6:36709800-36711400	Strong transcription	Fetal Stomach	stomach
28	chr6:36710000-36710600	Enhancers	Stomach Mucosa	stomach
29	chr6:36710000-36710800	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:36710000-36711000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:36710200-36710400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:36710200-36710600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr6:36710200-36715600	Weak transcription	Fetal Brain Female	brain

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