Variant report

Variant	rs10851411
Chromosome Location	chr15:42859235-42859236
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42854171..42864590-chr15:42864872..42869799,12	K562	blood:
2	chr15:42854080..42855765-chr15:42858958..42860703,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC57-2	chr15:42859229-42859337	ENSG00000261822.1

Variant related genes	Relation type
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10454039	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1060291	0.90[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs10851410	0.86[CEU][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs11022	0.86[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs11070374	0.90[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631193	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636577	0.81[CEU][hapmap]
rs11638208	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1197547	0.82[MKK][hapmap]
rs12324113	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12324717	0.86[CEU][hapmap];0.85[TSI][hapmap];0.95[EUR][1000 genomes]
rs12903432	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906697	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1900921	0.86[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2241998	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2255995	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595939	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2595940	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2595941	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617236	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28886308	0.81[EUR][1000 genomes]
rs2899051	0.84[EUR][1000 genomes]
rs2899057	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34643746	0.95[EUR][1000 genomes]
rs3986280	0.86[CEU][hapmap];0.85[TSI][hapmap];0.95[EUR][1000 genomes]
rs4573906	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923947	0.81[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs4923948	0.86[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4924684	0.88[EUR][1000 genomes]
rs56357092	0.88[EUR][1000 genomes]
rs60380503	0.87[EUR][1000 genomes]
rs7168835	0.84[AMR][1000 genomes]
rs8033412	0.86[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs9302112	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10851411	SNAP23	cis	parietal	SCAN
rs10851411	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs10851411	RINT1	trans	cerebellum	SCAN
rs10851411	MAP1A	cis	parietal	SCAN
rs10851411	TMCO5A	cis	parietal	SCAN
rs10851411	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs10851411	MAP1A	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42841600-42866800	Weak transcription	Stomach Mucosa	stomach
2	chr15:42841800-42867000	Weak transcription	Ovary	ovary
3	chr15:42842200-42867000	Weak transcription	Psoas Muscle	Psoas
4	chr15:42842400-42867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42842600-42867400	Weak transcription	Small Intestine	intestine
6	chr15:42842800-42867000	Weak transcription	Fetal Kidney	kidney
7	chr15:42843000-42863000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42847000-42860000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:42848000-42861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:42848600-42861200	Strong transcription	Fetal Intestine Large	intestine
11	chr15:42849200-42861400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:42849400-42866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:42849600-42859600	Strong transcription	K562	blood
14	chr15:42849800-42859800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:42849800-42859800	Strong transcription	Dnd41	blood
16	chr15:42849800-42860000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:42849800-42860000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:42849800-42860400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:42849800-42861000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:42849800-42861200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:42849800-42861200	Strong transcription	GM12878-XiMat	blood
22	chr15:42849800-42862800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:42850000-42859400	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:42850000-42861400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr15:42850000-42862800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:42850200-42859800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:42850200-42859800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:42850200-42861000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:42850200-42861200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:42850200-42861200	Strong transcription	Primary T cells from cord blood	blood
31	chr15:42850400-42859800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:42850400-42861200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:42850400-42861200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:42850600-42859800	Strong transcription	Thymus	Thymus
35	chr15:42850600-42860600	Strong transcription	Fetal Intestine Small	intestine
36	chr15:42850600-42861200	Strong transcription	Fetal Thymus	thymus
37	chr15:42850800-42859600	Strong transcription	Fetal Muscle Leg	muscle
38	chr15:42850800-42861000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:42850800-42861000	Strong transcription	Brain Germinal Matrix	brain
40	chr15:42850800-42861000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr15:42850800-42861200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr15:42850800-42861400	Strong transcription	Adipose Nuclei	Adipose
43	chr15:42851000-42859400	Strong transcription	Primary B cells from cord blood	blood
44	chr15:42851000-42859400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:42851000-42859600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:42851000-42859600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:42851000-42859600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:42851000-42859600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:42851000-42860400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:42851000-42861000	Strong transcription	Primary T cells fromperipheralblood	blood

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