Variant report

Variant	rs10789621
Chromosome Location	chr11:107259071-107259072
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	chr11:107258832..107260455-chr11:107266741..107268577,2	K562	blood:

Extended variants
information (count: 129 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1046094	0.84[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1046095	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10502087	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10749896	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10749897	0.83[EUR][1000 genomes]
rs10749899	0.81[EUR][1000 genomes]
rs10749900	0.86[EUR][1000 genomes]
rs10749901	0.88[EUR][1000 genomes]
rs10749903	0.84[CEU][hapmap]
rs10789594	0.83[EUR][1000 genomes]
rs10789597	0.81[EUR][1000 genomes]
rs10789598	0.83[EUR][1000 genomes]
rs10789604	0.83[EUR][1000 genomes]
rs10789605	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10789606	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10789607	0.88[EUR][1000 genomes]
rs10789608	0.88[EUR][1000 genomes]
rs10789611	0.88[EUR][1000 genomes]
rs10789612	0.88[EUR][1000 genomes]
rs10789613	0.88[EUR][1000 genomes]
rs10789614	0.81[EUR][1000 genomes]
rs10789615	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10789616	0.91[CEU][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes]
rs10789617	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10789618	0.84[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs10789620	1.00[JPT][hapmap]
rs10890695	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10890696	0.83[EUR][1000 genomes]
rs10890697	0.83[EUR][1000 genomes]
rs10890699	0.83[EUR][1000 genomes]
rs10890701	0.81[EUR][1000 genomes]
rs10890704	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10890705	0.88[EUR][1000 genomes]
rs10890706	0.84[EUR][1000 genomes]
rs10890707	0.88[EUR][1000 genomes]
rs10890708	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10890709	0.88[EUR][1000 genomes]
rs10890711	0.85[EUR][1000 genomes]
rs10890712	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10890715	0.88[EUR][1000 genomes]
rs10890716	0.88[EUR][1000 genomes]
rs10890718	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890719	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890720	0.86[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890721	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890723	0.92[ASN][1000 genomes]
rs11212132	0.81[EUR][1000 genomes]
rs11212138	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11212141	0.83[EUR][1000 genomes]
rs11212142	0.83[EUR][1000 genomes]
rs11212143	0.83[EUR][1000 genomes]
rs11212150	0.83[EUR][1000 genomes]
rs11212153	0.87[EUR][1000 genomes]
rs11212156	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11212157	0.88[EUR][1000 genomes]
rs11212158	0.88[EUR][1000 genomes]
rs11212159	0.88[EUR][1000 genomes]
rs11212160	0.88[EUR][1000 genomes]
rs11212162	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11212164	0.88[EUR][1000 genomes]
rs11212166	1.00[JPT][hapmap]
rs11212173	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11212175	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11212177	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11212179	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11212180	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11212181	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11212182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11212197	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11212206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11212207	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs11602033	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604771	0.83[EUR][1000 genomes]
rs11607304	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146472	0.87[EUR][1000 genomes]
rs12146473	0.88[EUR][1000 genomes]
rs12270655	0.85[EUR][1000 genomes]
rs12285491	0.94[ASN][1000 genomes]
rs12285607	0.83[EUR][1000 genomes]
rs12286342	0.88[EUR][1000 genomes]
rs12286915	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs12290112	0.84[EUR][1000 genomes]
rs1490945	0.88[EUR][1000 genomes]
rs17106875	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2046903	0.88[EUR][1000 genomes]
rs2161965	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2355840	0.83[EUR][1000 genomes]
rs2356280	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758911	0.84[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4343000	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4387327	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4576794	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517240	0.84[AFR][1000 genomes]
rs520203	0.84[LWK][hapmap]
rs55837508	0.88[EUR][1000 genomes]
rs56393657	0.94[ASN][1000 genomes]
rs56753250	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs588921	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs590699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59525924	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6421541	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs655448	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6588964	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6588965	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs671493	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs687991	0.86[ASN][1000 genomes]
rs7117615	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7131522	0.83[EUR][1000 genomes]
rs72990438	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72990443	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7350479	0.94[ASN][1000 genomes]
rs7358296	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7358308	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs999984	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs999985	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898364	chr11:106944975-107285636	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv898373	chr11:107124903-107433835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv832261	chr11:107145901-107321562	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv898374	chr11:107156880-107263130	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv2756363	chr11:107189790-107376790	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv556376	chr11:107250851-107486598	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10789621	LRRC50	trans	cerebellum	SCAN
rs10789621	CWF19L2	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107195000-107299200	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:107223000-107260600	Weak transcription	Brain Anterior Caudate	brain
3	chr11:107223000-107260600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:107230200-107261400	Weak transcription	Ovary	ovary
5	chr11:107240600-107261800	Weak transcription	Fetal Lung	lung
6	chr11:107241600-107261200	Weak transcription	Fetal Kidney	kidney
7	chr11:107241600-107327800	Weak transcription	HSMMtube	muscle
8	chr11:107243800-107267600	Weak transcription	Gastric	stomach
9	chr11:107247600-107259400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:107248000-107260000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:107248600-107260800	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:107248600-107261400	Weak transcription	Thymus	Thymus
13	chr11:107249000-107261000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:107249000-107267600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:107249200-107260000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:107249400-107260600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:107249800-107259600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:107250200-107260000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:107250200-107261800	Weak transcription	Psoas Muscle	Psoas
20	chr11:107251000-107260000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:107251400-107260800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:107251800-107260000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:107251800-107260000	Weak transcription	Placenta	Placenta
24	chr11:107252000-107259800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:107252000-107261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:107252000-107261000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:107252200-107260400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:107252200-107260400	Weak transcription	GM12878-XiMat	blood
29	chr11:107252400-107267800	Weak transcription	Right Ventricle	heart
30	chr11:107252600-107260000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:107252600-107267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:107252600-107281200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:107252600-107323800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:107253000-107261400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:107253000-107261400	Weak transcription	Pancreas	Pancrea
36	chr11:107253200-107260000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr11:107253600-107260000	Weak transcription	Fetal Thymus	thymus
38	chr11:107253600-107260600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:107253800-107260600	Weak transcription	HSMM	muscle
40	chr11:107254000-107260800	Weak transcription	Fetal Intestine Large	intestine
41	chr11:107254000-107261200	Weak transcription	Fetal Muscle Leg	muscle
42	chr11:107254200-107260400	Weak transcription	Dnd41	blood
43	chr11:107254200-107261400	Weak transcription	Left Ventricle	heart
44	chr11:107254200-107261400	Weak transcription	Lung	lung
45	chr11:107255000-107259600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr11:107255000-107327600	Weak transcription	Fetal Heart	heart
47	chr11:107256200-107261400	Weak transcription	Spleen	Spleen
48	chr11:107256600-107261000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:107256600-107261000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr11:107256600-107263000	Weak transcription	Brain Angular Gyrus	brain

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