Variant report

Variant	rs14419
Chromosome Location	chr9:116170559-116170560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:116170531-116170648	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:116168038-116171196	K562	blood:	n/a	n/a
3	POLR2A	chr9:116170255-116170656	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116135295..116143276-chr9:116169551..116176415,12	MCF-7	breast:
2	chr9:116069305..116071615-chr9:116169344..116170916,2	MCF-7	breast:
3	chr9:116065172..116068096-chr9:116167897..116170819,2	MCF-7	breast:
4	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
5	chr9:116116941..116119780-chr9:116168101..116172088,3	MCF-7	breast:
6	chr9:115983607..115986374-chr9:116170251..116172763,3	MCF-7	breast:
7	chr2:196521632..196523529-chr9:116170314..116172766,2	MCF-7	breast:
8	chr9:116169791..116174768-chr9:116341586..116346658,6	MCF-7	breast:
9	chr9:116162231..116166322-chr9:116170436..116174778,10	MCF-7	breast:
10	chr9:116035649..116038328-chr9:116169495..116171844,3	MCF-7	breast:
11	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
12	chr9:116137711..116140473-chr9:116169496..116173211,3	K562	blood:
13	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf43-1	chr9:116170093-116170738	NONHSAT134345

No data

Variant related genes	Relation type
C9orf43	TF binding region
ENSG00000136868	Chromatin interaction
ENSG00000196950	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000119431	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10733605	0.94[ASW][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap]
rs10739393	0.80[TSI][hapmap]
rs4979253	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs4979254	1.00[JPT][hapmap]
rs4979261	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs7037761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7875727	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs818692	0.92[ASN][1000 genomes]
rs818693	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs818694	1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs818696	0.82[ASN][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs14419	ALAD	Cis_1M	lymphoblastoid	RTeQTL
rs14419	TBC1D30	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116163600-116172200	Weak transcription	Small Intestine	intestine
2	chr9:116164000-116171000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:116164000-116171400	Weak transcription	Pancreas	Pancrea
4	chr9:116164000-116171600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:116164000-116171600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:116164200-116170800	Weak transcription	Fetal Brain Male	brain
7	chr9:116164200-116171200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:116164200-116171800	Weak transcription	Right Atrium	heart
9	chr9:116164200-116172000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:116164400-116170600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:116164400-116171600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:116164400-116171600	Weak transcription	Colonic Mucosa	Colon
13	chr9:116164400-116171600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:116164400-116171800	Weak transcription	Stomach Mucosa	stomach
15	chr9:116167400-116171400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:116169200-116171600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr9:116169200-116171600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:116169400-116170600	Genic enhancers	Hela-S3	cervix
19	chr9:116169400-116170800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr9:116169400-116171000	Strong transcription	Brain Anterior Caudate	brain
21	chr9:116169400-116171000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:116169400-116171000	Strong transcription	Fetal Brain Female	brain
23	chr9:116169400-116171200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:116169400-116171200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:116169400-116171200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:116169400-116171200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:116169400-116171200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:116169400-116171200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:116169400-116171200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:116169400-116171200	Genic enhancers	K562	blood
31	chr9:116169400-116171200	Strong transcription	NH-A	brain
32	chr9:116169400-116171200	Strong transcription	NHDF-Ad	bronchial
33	chr9:116169400-116171400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr9:116169400-116171400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:116169400-116171400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:116169400-116171400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:116169400-116171400	Genic enhancers	NHEK	skin
38	chr9:116169400-116171600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr9:116169400-116171600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:116169400-116171600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:116169400-116171600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:116169400-116171600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:116169400-116171600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:116169400-116171600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:116169400-116171600	Strong transcription	Placenta	Placenta
46	chr9:116169400-116171600	Strong transcription	HSMM	muscle
47	chr9:116169600-116170800	Strong transcription	Fetal Muscle Leg	muscle
48	chr9:116169600-116171000	Genic enhancers	Brain Germinal Matrix	brain
49	chr9:116169600-116171000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr9:116169600-116171200	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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