Variant report

Variant	rs1408503
Chromosome Location	chr6:33865119-33865120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:33864226-33865250	MCF-7	breast:	n/a	chr6:33864372-33864381
2	ESR1	chr6:33864613-33865188	T-47D	breast:	n/a	chr6:33864812-33864829
3	TCF7L2	chr6:33864732-33865198	MCF-7	breast:	n/a	n/a
4	GATA3	chr6:33864183-33865166	MCF-7	breast:	n/a	n/a
5	ESR1	chr6:33864562-33865155	T-47D	breast:	n/a	chr6:33864812-33864829
6	NR2F2	chr6:33864430-33865250	MCF-7	breast:	n/a	n/a
7	ESR1	chr6:33864574-33865122	T-47D	breast:	n/a	chr6:33864812-33864829
8	ESR1	chr6:33864537-33865133	T-47D	breast:	n/a	chr6:33864812-33864829

No.	Distal block	Cell Line	Cell type
1	chr6:33864193..33866303-chr6:33876209..33879014,2	MCF-7	breast:
2	chr6:33858737..33862272-chr6:33862763..33866214,4	MCF-7	breast:
3	chr6:33864701..33867431-chr6:33868454..33870776,4	K562	blood:
4	chr6:33863866..33866857-chr6:33868075..33870353,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233183	TF binding region
LINC01016	TF binding region
ENSG00000233183	Chromatin interaction
ENSG00000249346	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10807129	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs12209273	1.00[AFR][1000 genomes]
rs1324579	0.89[EUR][1000 genomes]
rs1535940	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1535941	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1535943	0.81[EUR][1000 genomes]
rs1535944	0.91[EUR][1000 genomes]
rs1535945	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1535946	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1535947	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1969843	0.85[EUR][1000 genomes]
rs2093907	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2147423	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2147426	0.90[EUR][1000 genomes]
rs2147427	0.89[EUR][1000 genomes]
rs2181916	0.86[EUR][1000 genomes]
rs2477228	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2477231	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2477232	0.90[EUR][1000 genomes]
rs2477235	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2477236	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2477237	0.90[EUR][1000 genomes]
rs2499737	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4711364	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs4711365	0.91[EUR][1000 genomes]
rs4713715	0.91[EUR][1000 genomes]
rs4713716	0.91[EUR][1000 genomes]
rs4713717	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs4713721	0.91[EUR][1000 genomes]
rs6457747	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs6921366	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs9296103	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9368781	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs942506	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs942508	0.91[EUR][1000 genomes]
rs942509	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs942510	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1408503	PFDN6	cis	brain	BrainEAC

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33850000-33871800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:33861600-33865200	Enhancers	Colon Smooth Muscle	Colon
3	chr6:33862400-33867000	Weak transcription	Spleen	Spleen
4	chr6:33862600-33865600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:33862800-33865600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:33862800-33865600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:33862800-33866000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr6:33862800-33866200	Enhancers	Fetal Thymus	thymus
9	chr6:33863000-33865200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:33863000-33865200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:33863000-33865400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr6:33863000-33865600	Enhancers	Primary T cells from cord blood	blood
13	chr6:33863000-33865600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr6:33863000-33865600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:33863200-33865800	Enhancers	Fetal Stomach	stomach
16	chr6:33863400-33865800	Enhancers	Fetal Intestine Large	intestine
17	chr6:33863600-33865200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:33863800-33865200	Enhancers	K562	blood
19	chr6:33863800-33865400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:33863800-33865400	Enhancers	Small Intestine	intestine
21	chr6:33863800-33865600	Enhancers	Duodenum Mucosa	Duodenum
22	chr6:33863800-33866400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:33864000-33865200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:33864000-33865800	Enhancers	Fetal Lung	lung
25	chr6:33864000-33870800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:33864200-33865600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr6:33864400-33865200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:33864400-33865400	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:33864400-33865400	Enhancers	A549	lung
30	chr6:33864400-33865600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:33864400-33865600	Enhancers	Rectal Smooth Muscle	rectum
32	chr6:33864400-33866000	Enhancers	Pancreas	Pancrea
33	chr6:33864600-33865200	Enhancers	Primary hematopoietic stem cells	blood
34	chr6:33864600-33865600	Enhancers	Esophagus	oesophagus
35	chr6:33864800-33865200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:33864800-33865400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:33864800-33865400	Bivalent Enhancer	HepG2	liver
38	chr6:33864800-33865600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr6:33864800-33865600	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:33864800-33865600	Enhancers	Thymus	Thymus
41	chr6:33864800-33866000	Enhancers	Fetal Intestine Small	intestine
42	chr6:33864800-33869600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:33865000-33865400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:33865000-33865600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr6:33865000-33865600	Enhancers	Placenta	Placenta
46	chr6:33865000-33865600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr6:33865000-33871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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