Variant report

Variant	rs3814226
Chromosome Location	chr10:97920062-97920063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97914380..97917567-chr10:97919091..97921187,3	K562	blood:
2	chr10:97848882..97852463-chr10:97918917..97921781,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNJ-1	chr10:97917647-97920099	ENSG00000177853
2	lnc-CCNJ-1	chr10:97915954-97920099	ENSG00000177853

Variant related genes	Relation type
ENSG00000226688	Chromatin interaction
ENSG00000177853	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10458746	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047370	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10509699	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10786262	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10882703	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10882714	0.80[ASN][1000 genomes]
rs10882716	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882717	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188549	0.86[EUR][1000 genomes]
rs11188550	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11188554	1.00[EUR][1000 genomes]
rs11188557	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11188566	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11188572	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188578	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11188580	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11188581	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11188582	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11188583	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188593	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188594	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11188595	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188598	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188599	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188603	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188616	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188639	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11188657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11814171	1.00[EUR][1000 genomes]
rs12219508	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12221239	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12414081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12569991	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12570955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12572217	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1336455	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17111275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974251	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2085492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4145226	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72474879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7898901	1.00[EUR][1000 genomes]
rs7913418	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs915506	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3814226	C2CD4B	trans	brain	seeQTL
rs3814226	CSF3	trans	brain	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97890800-97922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:97891000-97927000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:97891800-97921400	Weak transcription	Stomach Mucosa	stomach
4	chr10:97892400-97924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:97892800-97924200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:97903200-97923000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr10:97903600-97920200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:97910800-97920200	Strong transcription	Fetal Muscle Leg	muscle
9	chr10:97910800-97922200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr10:97911000-97920400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:97911000-97921000	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr10:97911000-97921200	Strong transcription	Primary B cells from cord blood	blood
13	chr10:97911000-97921800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:97911000-97921800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr10:97911000-97921800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr10:97911000-97922000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr10:97911000-97923000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr10:97912400-97920800	Weak transcription	Right Ventricle	heart
19	chr10:97912400-97927800	Weak transcription	Fetal Brain Male	brain
20	chr10:97913000-97920200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr10:97913000-97925400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:97913200-97920600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:97914200-97924800	Weak transcription	Fetal Intestine Small	intestine
24	chr10:97914200-97925600	Weak transcription	Fetal Stomach	stomach
25	chr10:97914200-97925800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:97914200-97926200	Weak transcription	Pancreas	Pancrea
27	chr10:97914600-97921800	Weak transcription	Brain Germinal Matrix	brain
28	chr10:97915000-97920400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr10:97915400-97923200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:97915400-97923400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr10:97916200-97921000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr10:97916400-97920400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:97917000-97920600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:97917200-97922200	Weak transcription	Colon Smooth Muscle	Colon
35	chr10:97917400-97920600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr10:97917400-97921600	Weak transcription	Colonic Mucosa	Colon
37	chr10:97917400-97922800	Weak transcription	Fetal Heart	heart
38	chr10:97917400-97923000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr10:97917400-97928000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr10:97917600-97920800	Weak transcription	Brain Anterior Caudate	brain
41	chr10:97917600-97922600	Weak transcription	Ovary	ovary
42	chr10:97917600-97924800	Weak transcription	Small Intestine	intestine
43	chr10:97917600-97925200	Weak transcription	Fetal Brain Female	brain
44	chr10:97917600-97925800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:97917800-97920800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr10:97917800-97920800	Weak transcription	NHDF-Ad	bronchial
47	chr10:97917800-97921600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr10:97918000-97923800	Weak transcription	HUVEC	blood vessel
49	chr10:97918000-97924200	Weak transcription	HSMM	muscle
50	chr10:97918000-97925400	Weak transcription	Brain Hippocampus Middle	brain

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