Variant report

Variant	rs6479447
Chromosome Location	chr9:95799446-95799447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95798879..95801785-chr9:95811313..95813235,2	MCF-7	breast:
2	chr9:95797721..95799808-chr9:95800868..95803137,2	MCF-7	breast:
3	chr9:95797648..95801708-chr9:95856413..95859083,5	MCF-7	breast:
4	chr9:95780776..95784501-chr9:95797559..95801380,3	MCF-7	breast:
5	chr9:95797817..95800116-chr9:95854194..95855844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10761191	0.85[CEU][hapmap]
rs10821058	0.85[CEU][hapmap]
rs4743879	0.86[EUR][1000 genomes]
rs6479446	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6479447	SUSD3	cis	multi-tissue	Pritchard
rs6479447	ZNF484	cis	cerebellum	SCAN
rs6479447	ZNF484	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95791000-95800400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:95791200-95799800	Strong transcription	Thymus	Thymus
3	chr9:95791400-95799800	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr9:95791400-95800000	Genic enhancers	Primary monocytes fromperipheralblood	blood
5	chr9:95791400-95800000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:95791800-95799800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr9:95792000-95800000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr9:95794400-95800000	Weak transcription	Liver	Liver
9	chr9:95795000-95799800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
10	chr9:95795200-95800400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:95795200-95801400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:95796600-95800400	Weak transcription	Fetal Intestine Large	intestine
13	chr9:95797400-95800800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:95798000-95802400	Weak transcription	Gastric	stomach
15	chr9:95798200-95799600	Genic enhancers	Primary T cells from cord blood	blood
16	chr9:95798200-95800600	Weak transcription	Fetal Brain Female	brain
17	chr9:95798200-95800800	Enhancers	Primary hematopoietic stem cells	blood
18	chr9:95798400-95799600	Weak transcription	Primary B cells from cord blood	blood
19	chr9:95798400-95799600	Weak transcription	K562	blood
20	chr9:95798400-95800200	Weak transcription	Brain Germinal Matrix	brain
21	chr9:95798400-95801400	Enhancers	Placenta	Placenta
22	chr9:95798400-95801800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr9:95798600-95800400	Enhancers	Fetal Muscle Trunk	muscle
24	chr9:95798600-95800600	Weak transcription	Dnd41	blood
25	chr9:95798800-95799800	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr9:95798800-95800200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr9:95798800-95804200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr9:95799000-95799600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:95799000-95799800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:95799000-95800200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr9:95799000-95800200	Weak transcription	Lung	lung
32	chr9:95799000-95800800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:95799200-95799600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:95799200-95799600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:95799200-95799800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:95799200-95799800	Genic enhancers	Fetal Stomach	stomach
37	chr9:95799200-95800000	Weak transcription	Fetal Intestine Small	intestine
38	chr9:95799200-95800400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:95799200-95800600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:95799200-95800600	Enhancers	Adipose Nuclei	Adipose
41	chr9:95799200-95800800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:95799200-95800800	Enhancers	Fetal Thymus	thymus
43	chr9:95799200-95801000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:95799400-95799600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr9:95799400-95799800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:95799400-95799800	Genic enhancers	Spleen	Spleen
47	chr9:95799400-95800000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
48	chr9:95799400-95800200	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:95799400-95800200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr9:95799400-95800400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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