Variant report

Variant	rs12978323
Chromosome Location	chr19:41756038-41756039
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41754992..41757426-chr19:41761264..41763362,2	MCF-7	breast:
2	chr19:41743047..41745735-chr19:41754971..41757582,2	K562	blood:
3	chr19:41755140..41756874-chr19:41768060..41770333,2	MCF-7	breast:
4	chr19:41748141..41750709-chr19:41755527..41757688,2	K562	blood:
5	chr19:41731239..41733733-chr19:41753388..41756515,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167601	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10410836	0.83[ASN][1000 genomes]
rs10421990	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11879435	0.84[CHB][hapmap]
rs11879562	0.85[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11882467	0.88[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12327659	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12462203	0.85[CHB][hapmap]
rs12974323	0.81[ASN][1000 genomes]
rs12975585	0.94[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs12975920	0.82[ASN][1000 genomes]
rs12980267	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs12980480	0.85[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12983047	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12983339	0.86[EUR][1000 genomes]
rs13345456	0.81[ASN][1000 genomes]
rs1865051	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1865053	0.85[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1946612	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs1946613	0.84[CHB][hapmap]
rs2304230	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2304231	0.84[CHB][hapmap]
rs2304232	0.85[CHB][hapmap]
rs2304234	0.83[ASW][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs3745295	0.85[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3752705	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3760659	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs3760660	0.85[CHB][hapmap]
rs3816052	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3826714	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4456618	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4591267	0.85[CHB][hapmap]
rs4802111	0.85[CHB][hapmap]
rs4802112	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs4802113	0.85[CHB][hapmap]
rs4802115	0.88[EUR][1000 genomes]
rs4803448	0.85[CHB][hapmap]
rs4803449	0.85[CHB][hapmap]
rs4803451	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6508974	0.85[CHB][hapmap]
rs66724427	0.83[ASN][1000 genomes]
rs6957	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7245398	0.85[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7246525	0.85[CHB][hapmap]
rs7248164	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7250883	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs7256416	0.83[ASN][1000 genomes]
rs7256856	0.81[ASN][1000 genomes]
rs7257310	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs7257825	0.83[ASN][1000 genomes]
rs7258749	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs8105161	0.87[JPT][hapmap]
rs8109167	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs8109627	0.81[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12978323	PLEKHA4	cis	cerebellum	SCAN
rs12978323	FOXA3	cis	cerebellum	SCAN
rs12978323	BAX	cis	cerebellum	SCAN
rs12978323	SLC6A16	cis	cerebellum	SCAN
rs12978323	TSKS	cis	parietal	SCAN
rs12978323	SLC1A5	cis	parietal	SCAN
rs12978323	SLC1A5	cis	cerebellum	SCAN
rs12978323	AXL	cis	Liver	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
3	chr19:41733200-41767200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:41733200-41767200	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr19:41736000-41767200	Strong transcription	Osteobl	bone
6	chr19:41736000-41767400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:41736200-41757000	Strong transcription	NH-A	brain
8	chr19:41736400-41767800	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr19:41736600-41757200	Strong transcription	NHLF	lung
10	chr19:41736600-41766200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:41736600-41766600	Strong transcription	Fetal Stomach	stomach
12	chr19:41736600-41767000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:41736600-41767200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:41736600-41767400	Strong transcription	HSMM	muscle
15	chr19:41736600-41767800	Weak transcription	Brain Angular Gyrus	brain
16	chr19:41736800-41758200	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:41736800-41762400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:41737200-41766000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr19:41737400-41766600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:41738000-41761000	Strong transcription	Colon Smooth Muscle	Colon
21	chr19:41738800-41767400	Weak transcription	Fetal Brain Male	brain
22	chr19:41739400-41758200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:41739400-41767400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:41739800-41766200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:41742600-41767600	Strong transcription	A549	lung
26	chr19:41742800-41757000	Strong transcription	HSMMtube	muscle
27	chr19:41742800-41757200	Strong transcription	Ovary	ovary
28	chr19:41743000-41757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:41743400-41757200	Strong transcription	HUVEC	blood vessel
30	chr19:41743600-41758400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:41743800-41761200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr19:41745200-41765000	Weak transcription	Fetal Brain Female	brain
33	chr19:41745600-41756600	Weak transcription	Stomach Mucosa	stomach
34	chr19:41745600-41760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:41745800-41758200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:41745800-41762200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr19:41745800-41767200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:41746400-41756800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr19:41746800-41758200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:41749600-41758200	Weak transcription	Right Ventricle	heart
41	chr19:41749600-41758400	Weak transcription	Spleen	Spleen
42	chr19:41749800-41756200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:41753200-41757200	Strong transcription	Aorta	Aorta
44	chr19:41753400-41767000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:41753800-41759800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:41753800-41767400	Strong transcription	NHDF-Ad	bronchial
47	chr19:41754000-41756400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:41754000-41756800	Strong transcription	Colonic Mucosa	Colon
49	chr19:41754000-41757000	Strong transcription	Adipose Nuclei	Adipose
50	chr19:41754000-41757200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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