Variant report

Variant	rs4362075
Chromosome Location	chr10:865476-865477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:864554-866546	GM12891	blood:	n/a	n/a
2	POLR2A	chr10:865319-865633	K562	blood:	n/a	n/a
3	POLR2A	chr10:865433-865575	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr10:862184-870670	K562	blood:	n/a	n/a
5	POLR2A	chr10:865340-866260	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:864445..868005-chr10:868654..872720,4	MCF-7	breast:
2	chr10:860534..862520-chr10:865171..867219,2	MCF-7	breast:

Variant related genes	Relation type
LARP4B	TF binding region
ENSG00000107929	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1000278	0.87[ASN][1000 genomes]
rs1057303	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1057304	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10752020	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10752021	0.90[CHB][hapmap]
rs10904571	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10904572	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10904575	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11253448	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11253449	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11253451	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11253471	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12243303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.81[ASN][1000 genomes]
rs12413228	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12413763	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12573825	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12774722	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1536338	0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs1555897	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1555898	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2148368	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2274376	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2892159	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763722	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4097329	0.83[EUR][1000 genomes]
rs4229	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4880743	0.95[CHB][hapmap];0.85[YRI][hapmap]
rs4881532	0.81[ASN][1000 genomes]
rs4881535	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4881538	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61831437	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61831439	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7069505	0.82[CHD][hapmap]
rs7071801	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7077992	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs7080989	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs7091806	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs748112	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs749297	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs752375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7703	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap]
rs7899871	0.95[CHB][hapmap]
rs7913077	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7919815	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9124	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs997615	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
7	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	nsv948602	chr10:708293-944641	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	41 gene(s)	inside rSNPs	diseases
15	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1048707	chr10:834439-915534	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
17	nsv466698	chr10:836115-888073	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv549766	chr10:836115-888073	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4362075	LARP5	Cis_1M	lymphoblastoid	RTeQTL
rs4362075	DIP2C	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:849600-877800	Strong transcription	Fetal Intestine Small	intestine
2	chr10:850800-877800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:851000-883000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:851200-867000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr10:851200-872400	Strong transcription	Stomach Smooth Muscle	stomach
6	chr10:851200-877800	Strong transcription	Fetal Stomach	stomach
7	chr10:851400-867200	Strong transcription	Placenta	Placenta
8	chr10:851400-878600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:851600-867200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:851600-872800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:851600-876600	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:851600-883000	Strong transcription	Fetal Intestine Large	intestine
13	chr10:851600-889800	Strong transcription	Dnd41	blood
14	chr10:851600-890800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr10:851600-895600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:851800-865600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:851800-867800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:851800-868000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:851800-877800	Strong transcription	Liver	Liver
20	chr10:851800-879000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:851800-894000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:851800-895800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr10:852000-868000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:852000-872400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr10:852000-876200	Strong transcription	Ovary	ovary
26	chr10:852000-877200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:852000-882800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:852200-872800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:852200-877800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr10:852200-956400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr10:852400-867200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr10:852400-875600	Strong transcription	Thymus	Thymus
33	chr10:852400-876800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:852400-877800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr10:852600-867800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr10:852600-877600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr10:852600-883400	Strong transcription	Primary T cells from cord blood	blood
38	chr10:852800-869000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr10:852800-869000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:852800-872200	Strong transcription	Rectal Smooth Muscle	rectum
41	chr10:852800-891800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:852800-894600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr10:852800-895000	Strong transcription	Fetal Thymus	thymus
44	chr10:853000-868600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr10:853000-869000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr10:853000-876000	Strong transcription	HUVEC	blood vessel
47	chr10:853000-876400	Strong transcription	A549	lung
48	chr10:853000-876600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr10:853000-876600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:853000-877600	Strong transcription	NHEK	skin

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