Variant report

Variant	rs10778476
Chromosome Location	chr12:106855733-106855734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-144F15.1.1-1	chr12:106854483-106856139	ENSG00000250518

Extended variants
information (count: 159 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10047654	0.88[ASN][1000 genomes]
rs10444532	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10507211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10746059	0.91[ASN][1000 genomes]
rs10746060	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10778465	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778466	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778468	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778469	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778470	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778471	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778473	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778474	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778475	0.88[ASN][1000 genomes]
rs10778478	0.88[ASN][1000 genomes]
rs10778480	0.88[ASN][1000 genomes]
rs10778481	0.88[ASN][1000 genomes]
rs10778485	0.86[AMR][1000 genomes]
rs10861577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861578	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861579	0.88[EUR][1000 genomes]
rs10861580	0.80[ASN][1000 genomes]
rs10861581	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861582	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10861585	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861586	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861587	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10861588	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10861589	0.80[ASN][1000 genomes]
rs10861590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861592	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861594	0.88[ASN][1000 genomes]
rs10861595	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861597	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10861598	0.88[ASN][1000 genomes]
rs10861599	0.88[ASN][1000 genomes]
rs10861601	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861604	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861605	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861608	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861609	0.88[ASN][1000 genomes]
rs10861613	0.85[ASN][1000 genomes]
rs10861614	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11112933	1.00[CHB][hapmap]
rs11112940	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112945	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11112952	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11112953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112957	0.80[ASN][1000 genomes]
rs11112961	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112971	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112979	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112980	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112986	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112990	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112991	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112992	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112993	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112995	0.88[ASN][1000 genomes]
rs11113003	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113004	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113009	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134577	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11609315	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611176	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611252	0.88[ASN][1000 genomes]
rs11611815	0.80[EUR][1000 genomes]
rs11615682	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11835357	0.88[ASN][1000 genomes]
rs11835362	1.00[ASN][1000 genomes]
rs12298876	0.88[ASN][1000 genomes]
rs12305705	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12309708	0.88[ASN][1000 genomes]
rs12309758	0.88[ASN][1000 genomes]
rs12312915	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12422988	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12423068	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424952	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12425459	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17038414	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17218490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17284674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17285274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1921952	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2141774	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2243455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2288268	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2374606	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374610	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28475238	0.85[AMR][1000 genomes]
rs2888888	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2900499	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2900500	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34955444	0.91[ASN][1000 genomes]
rs3851631	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851632	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851633	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4509864	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4522273	0.86[AMR][1000 genomes]
rs4625578	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55678155	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55689816	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60635749	0.88[ASN][1000 genomes]
rs61941917	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941918	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941920	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941921	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941922	0.88[ASN][1000 genomes]
rs61941943	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941944	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943670	0.88[EUR][1000 genomes]
rs61943672	0.91[ASN][1000 genomes]
rs61943690	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943693	0.96[ASN][1000 genomes]
rs61943694	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539268	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539269	0.88[ASN][1000 genomes]
rs6539270	0.88[ASN][1000 genomes]
rs6539271	0.88[ASN][1000 genomes]
rs67911933	0.80[ASN][1000 genomes]
rs67966244	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132744	0.86[EUR][1000 genomes]
rs7132971	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134615	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7134881	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs7135054	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7136098	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137445	0.88[ASN][1000 genomes]
rs7139139	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7139249	0.88[ASN][1000 genomes]
rs7296090	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7297873	0.88[ASN][1000 genomes]
rs7298062	0.82[EUR][1000 genomes]
rs7303873	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306012	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7306277	0.88[ASN][1000 genomes]
rs7306326	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7307711	0.88[AMR][1000 genomes]
rs7308541	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7309020	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310703	0.91[ASN][1000 genomes]
rs7311957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7315549	0.88[ASN][1000 genomes]
rs7961133	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7963213	0.88[ASN][1000 genomes]
rs7965520	0.88[ASN][1000 genomes]
rs7969743	0.88[ASN][1000 genomes]
rs7971581	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976305	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10778476	ANO1	trans	parietal	SCAN
rs10778476	CKAP4	cis	cerebellum	SCAN
rs10778476	STAB2	cis	parietal	SCAN
rs10778476	POLR3B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106787600-106856600	Weak transcription	GM12878-XiMat	blood
2	chr12:106813000-106864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:106813200-106855800	Weak transcription	NHDF-Ad	bronchial
4	chr12:106813200-106864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:106814400-106855800	Weak transcription	Stomach Mucosa	stomach
6	chr12:106823200-106858000	Weak transcription	Psoas Muscle	Psoas
7	chr12:106824800-106866400	Weak transcription	NHLF	lung
8	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:106828800-106855800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:106828800-106856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:106829000-106867200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:106830400-106864600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:106830400-106865800	Weak transcription	K562	blood
14	chr12:106831200-106856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:106831600-106856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:106831600-106856400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:106833000-106864400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:106840000-106864600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:106841800-106865000	Weak transcription	A549	lung
20	chr12:106846400-106864000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:106846400-106864600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:106846800-106856000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:106847400-106856000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:106848400-106855800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:106848400-106856000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:106848400-106856800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:106849000-106859400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:106849400-106856000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:106849600-106859400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:106849800-106857000	Weak transcription	Fetal Brain Male	brain
31	chr12:106850000-106856200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:106850400-106857000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:106850400-106858200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:106850600-106856000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:106850600-106856000	Strong transcription	Primary B cells from cord blood	blood
36	chr12:106851000-106864800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:106851200-106856000	Strong transcription	Adipose Nuclei	Adipose
38	chr12:106851200-106857400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:106851400-106855800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:106851400-106856000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:106851400-106856000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:106851400-106856000	Strong transcription	Placenta	Placenta
43	chr12:106851400-106856000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:106851400-106856000	Strong transcription	Spleen	Spleen
45	chr12:106851400-106858400	Strong transcription	Liver	Liver
46	chr12:106851400-106858400	Strong transcription	Fetal Muscle Leg	muscle
47	chr12:106851600-106855800	Strong transcription	Ovary	ovary
48	chr12:106851600-106856000	Strong transcription	Aorta	Aorta
49	chr12:106851600-106856000	Strong transcription	Fetal Intestine Large	intestine
50	chr12:106851600-106856000	Strong transcription	Rectal Mucosa Donor 29	rectum

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