Variant report

Variant	rs13407983
Chromosome Location	chr2:47233048-47233049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr2:47232942-47233081	K562	blood:	n/a	n/a
2	RCOR1	chr2:47232929-47233232	K562	blood:	n/a	n/a
3	TEAD4	chr2:47232830-47233214	K562	blood:	n/a	n/a
4	RCOR1	chr2:47232838-47233248	K562	blood:	n/a	n/a
5	EP300	chr2:47232850-47233154	K562	blood:	n/a	n/a
6	CEBPB	chr2:47232915-47233121	K562	blood:	n/a	n/a
7	CCNT2	chr2:47232922-47233102	K562	blood:	n/a	n/a
8	POLR2A	chr2:47233022-47233289	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:47232867-47233158	K562	blood:	n/a	n/a
10	MAZ	chr2:47232878-47233142	K562	blood:	n/a	n/a
11	POLR2A	chr2:47232923-47233115	K562	blood:	n/a	n/a
12	POLR2A	chr2:47233006-47233251	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:47232943-47233277	Hela-S3	cervix:	n/a	n/a
14	TEAD4	chr2:47232786-47233166	K562	blood:	n/a	n/a
15	TAL1	chr2:47232752-47233206	K562	blood:	n/a	n/a
16	ZMIZ1	chr2:47232979-47233109	K562	blood:	n/a	n/a
17	HMGN3	chr2:47232903-47233153	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47232895..47237077-chr2:47401374..47404385,4	MCF-7	breast:

No data

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10193261	0.91[LWK][hapmap]
rs10194115	0.85[LWK][hapmap]
rs13424540	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13426848	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55839799	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7570810	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv517929	chr2:47217094-47243312	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13407983	MSH2	cis	cerebellum	SCAN
rs13407983	SOCS5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47214200-47235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47214600-47242000	Strong transcription	Thymus	Thymus
5	chr2:47214800-47233400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:47214800-47237200	Strong transcription	Primary T cells from cord blood	blood
7	chr2:47214800-47239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:47215200-47243800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:47215400-47235800	Strong transcription	Primary B cells from cord blood	blood
10	chr2:47215600-47245200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:47216400-47241600	Strong transcription	Fetal Thymus	thymus
12	chr2:47219600-47235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
14	chr2:47223200-47235800	Weak transcription	Fetal Kidney	kidney
15	chr2:47223400-47238400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:47223400-47239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:47223600-47235600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:47223600-47239400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:47223600-47246800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:47223800-47234200	Weak transcription	Psoas Muscle	Psoas
21	chr2:47224200-47233200	Weak transcription	GM12878-XiMat	blood
22	chr2:47224800-47238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:47227400-47233200	Enhancers	Brain Angular Gyrus	brain
24	chr2:47227400-47234000	Enhancers	Brain Cingulate Gyrus	brain
25	chr2:47228400-47233200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:47229000-47233200	Enhancers	Fetal Muscle Leg	muscle
27	chr2:47229200-47243000	Enhancers	Fetal Brain Male	brain
28	chr2:47229200-47248600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:47229400-47235600	Enhancers	Fetal Brain Female	brain
30	chr2:47229600-47233200	Enhancers	Right Atrium	heart
31	chr2:47229600-47237000	Genic enhancers	Fetal Stomach	stomach
32	chr2:47230200-47234800	Strong transcription	Pancreas	Pancrea
33	chr2:47230200-47235800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:47230200-47236600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:47230200-47302800	Strong transcription	Dnd41	blood
36	chr2:47230400-47233200	Enhancers	Colon Smooth Muscle	Colon
37	chr2:47230400-47233200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:47230400-47235600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:47230600-47233200	Weak transcription	Fetal Lung	lung
40	chr2:47230600-47235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:47230600-47235400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:47230600-47235800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:47230600-47236600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:47230800-47233200	Enhancers	Stomach Smooth Muscle	stomach
45	chr2:47230800-47243000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:47231000-47233600	Enhancers	K562	blood
47	chr2:47231200-47235200	Strong transcription	Fetal Intestine Small	intestine
48	chr2:47231200-47235400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr2:47231400-47233800	Weak transcription	Stomach Mucosa	stomach
50	chr2:47231400-47235000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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