Variant report

Variant	rs6485802
Chromosome Location	chr11:48051442-48051443
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:48026525..48028849-chr11:48051139..48053523,2	MCF-7	breast:
2	chr11:48049637..48052585-chr11:48057175..48059884,2	K562	blood:
3	chr11:48015448..48018346-chr11:48050967..48053426,2	MCF-7	breast:
4	chr11:48001648..48004454-chr11:48049708..48052046,2	MCF-7	breast:
5	chr11:48042672..48045138-chr11:48049010..48052417,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149177	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10734561	0.81[CHB][hapmap]
rs10769312	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs10769313	0.81[CHB][hapmap]
rs10838798	0.82[CHB][hapmap]
rs10838800	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs10838802	0.81[CHB][hapmap]
rs11039530	1.00[YRI][hapmap]
rs11039543	1.00[YRI][hapmap]
rs1113480	0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs11601310	0.82[CHD][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap]
rs1228044	0.86[ASN][1000 genomes]
rs1566732	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs1631174	0.81[ASN][1000 genomes]
rs1681630	0.81[GIH][hapmap];0.85[MEX][hapmap]
rs2870080	1.00[YRI][hapmap]
rs2930196	0.97[ASN][1000 genomes]
rs34895872	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34972471	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4298856	1.00[YRI][hapmap]
rs4752805	0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4752894	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs4752904	1.00[YRI][hapmap]
rs4752907	1.00[YRI][hapmap]
rs7106731	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7130876	0.96[GIH][hapmap]
rs7395231	0.82[CHB][hapmap]
rs7479361	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs7927965	1.00[YRI][hapmap]
rs7934659	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[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	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6485802	ATG13	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48035600-48053000	Weak transcription	Thymus	Thymus
2	chr11:48035600-48056600	Weak transcription	HSMM	muscle
3	chr11:48038000-48052400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:48040600-48053200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:48040800-48053000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:48043600-48052800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:48045000-48053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:48046400-48056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:48046400-48058200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:48046600-48059600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:48047000-48057800	Weak transcription	NHLF	lung
12	chr11:48047200-48053000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:48047400-48051800	Weak transcription	Psoas Muscle	Psoas
14	chr11:48047400-48052400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:48047400-48052800	Weak transcription	Right Atrium	heart
16	chr11:48047400-48073400	Weak transcription	HSMMtube	muscle
17	chr11:48047400-48073800	Weak transcription	Left Ventricle	heart
18	chr11:48047600-48053000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:48047600-48055600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:48047800-48052400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:48047800-48053200	Weak transcription	Fetal Brain Female	brain
22	chr11:48047800-48055000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:48048000-48056600	Weak transcription	Pancreas	Pancrea
24	chr11:48048000-48057200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:48049000-48051800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr11:48049000-48058600	Genic enhancers	A549	lung
27	chr11:48049400-48056600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr11:48049600-48051600	Enhancers	Brain Substantia Nigra	brain
29	chr11:48049600-48051800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr11:48049600-48053200	Weak transcription	Colonic Mucosa	Colon
31	chr11:48049600-48054200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:48049800-48051600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr11:48049800-48051800	Enhancers	Primary T cells from cord blood	blood
34	chr11:48049800-48051800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr11:48049800-48051800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:48049800-48052200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr11:48049800-48052200	Enhancers	Gastric	stomach
38	chr11:48049800-48053000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr11:48049800-48054400	Enhancers	Stomach Mucosa	stomach
40	chr11:48050200-48052000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:48050200-48052200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:48050200-48052800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:48050200-48068200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:48050400-48051600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:48050400-48051600	Enhancers	HUVEC	blood vessel
46	chr11:48050400-48051800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr11:48050400-48052000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr11:48050400-48052000	Enhancers	NHDF-Ad	bronchial
49	chr11:48050400-48052200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:48050400-48052200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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