Variant report

Variant	rs10838805
Chromosome Location	chr11:48118993-48118994
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1039481	0.87[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs10734562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742828	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10742829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10742831	1.00[ASN][1000 genomes]
rs10742834	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs10742836	0.85[CEU][hapmap]
rs10769313	0.81[CEU][hapmap]
rs10769316	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838814	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs10838833	0.93[JPT][hapmap]
rs10838835	0.93[JPT][hapmap]
rs11039515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039519	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039520	0.85[ASN][1000 genomes]
rs11039538	0.81[ASN][1000 genomes]
rs11603850	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12289516	0.92[JPT][hapmap]
rs1503188	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1532754	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1566728	0.93[JPT][hapmap]
rs1566729	0.93[JPT][hapmap]
rs16905753	0.93[JPT][hapmap]
rs17198985	0.93[JPT][hapmap]
rs1875696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910364	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1969093	1.00[ASN][1000 genomes]
rs2047812	0.93[JPT][hapmap]
rs2174129	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2270990	0.87[CEU][hapmap]
rs2270993	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2279822	0.85[ASN][1000 genomes]
rs2279823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741410	0.93[JPT][hapmap]
rs3942852	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4597030	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs4752806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4752807	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752808	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752897	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4752900	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4752901	0.93[ASN][1000 genomes]
rs6485806	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6485809	0.98[ASN][1000 genomes]
rs7113857	0.86[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs7117386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7120775	0.93[JPT][hapmap]
rs7129364	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7947811	0.92[JPT][hapmap]
rs7948129	0.93[JPT][hapmap]
rs905475	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905477	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924715	0.87[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
15	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1048554	chr11:48062861-48388686	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1038210	chr11:48068862-48388686	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
19	nsv1052076	chr11:48077864-48702549	ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	nsv1053528	chr11:48086151-48125731	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
21	nsv869354	chr11:48088580-48783113	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	nsv1045734	chr11:48089315-48893207	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
23	nsv467871	chr11:48106486-48694871	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
24	nsv554211	chr11:48106486-48694871	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
25	nsv948502	chr11:48110043-48891877	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10838805	PTPRJ	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48103600-48122800	Weak transcription	Right Ventricle	heart
2	chr11:48105800-48121400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr11:48108800-48125400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:48110200-48121200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:48111000-48125400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:48111400-48121400	Weak transcription	Primary T cells from cord blood	blood
7	chr11:48111800-48121600	Weak transcription	Primary B cells from cord blood	blood
8	chr11:48112800-48121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:48113800-48125400	Enhancers	Brain Hippocampus Middle	brain
10	chr11:48114000-48119800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr11:48114200-48119000	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:48114200-48120000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr11:48114600-48131400	Weak transcription	Esophagus	oesophagus
14	chr11:48115800-48119000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr11:48115800-48121000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:48115800-48127400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:48116000-48119200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr11:48116000-48121600	Weak transcription	GM12878-XiMat	blood
19	chr11:48116200-48127400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:48116400-48121400	Enhancers	Liver	Liver
21	chr11:48116400-48122000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:48116400-48125600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:48116400-48128600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:48116600-48121400	Enhancers	HepG2	liver
25	chr11:48116600-48121600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr11:48116600-48122600	Weak transcription	Small Intestine	intestine
27	chr11:48116600-48122800	Weak transcription	Colonic Mucosa	Colon
28	chr11:48116600-48122800	Weak transcription	Left Ventricle	heart
29	chr11:48116600-48131200	Weak transcription	Psoas Muscle	Psoas
30	chr11:48117200-48119000	Enhancers	Pancreas	Pancrea
31	chr11:48117400-48119000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr11:48117400-48119000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:48117400-48119800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:48117400-48119800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr11:48117400-48119800	Enhancers	Stomach Mucosa	stomach
36	chr11:48117400-48120000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr11:48117400-48120000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr11:48117400-48120000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr11:48117400-48120000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:48117400-48120000	Enhancers	Placenta	Placenta
41	chr11:48117400-48120200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr11:48117400-48120200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:48117400-48122800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:48117600-48119000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:48117600-48119000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:48117600-48119000	Enhancers	Fetal Lung	lung
47	chr11:48117600-48119200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:48117600-48119200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:48117600-48119200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr11:48117600-48119600	Enhancers	H9 Cell Line	embryonic stem cell

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