Variant report

Variant	rs10899807
Chromosome Location	chr10:43947627-43947628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:
2	chr10:43911252..43915931-chr10:43947419..43953058,11	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FXYD4-4	chr10:43947368-43950112	NONHSAT012969

Variant related genes	Relation type
ENSG00000221400	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899791	0.84[ASN][1000 genomes]
rs10899793	0.84[ASN][1000 genomes]
rs10899794	0.90[JPT][hapmap]
rs10899796	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899797	0.90[JPT][hapmap]
rs10899800	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899801	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899802	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899806	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899808	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238525	0.82[ASN][1000 genomes]
rs11238530	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11238532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238558	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238566	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238572	0.88[AMR][1000 genomes]
rs11525297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11814409	0.85[CHB][hapmap];0.83[YRI][hapmap]
rs11815101	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12217904	0.82[YRI][hapmap]
rs12220230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220528	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12245541	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12250140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12254798	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12261855	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12262836	0.88[AMR][1000 genomes]
rs13376803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13376924	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17153534	0.84[ASN][1000 genomes]
rs2247979	0.90[JPT][hapmap]
rs2247981	0.90[JPT][hapmap]
rs2250444	0.90[JPT][hapmap]
rs2252783	0.80[JPT][hapmap]
rs2261636	0.90[JPT][hapmap]
rs28865415	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4648316	0.84[ASN][1000 genomes]
rs4948726	0.90[JPT][hapmap]
rs59383062	0.84[ASN][1000 genomes]
rs59806733	0.85[ASN][1000 genomes]
rs6593513	0.81[JPT][hapmap]
rs7099802	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7905676	0.90[JPT][hapmap]
rs7907179	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7921001	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	esv3448813	chr10:43919995-43950867	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1043746	chr10:43940898-43977155	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43933000-43949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:43933000-43950200	Weak transcription	Lung	lung
3	chr10:43933200-43948000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:43933200-43950000	Weak transcription	Brain Substantia Nigra	brain
5	chr10:43933200-43950200	Weak transcription	Brain Angular Gyrus	brain
6	chr10:43933200-43950200	Weak transcription	Brain Hippocampus Middle	brain
7	chr10:43933200-43950200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr10:43933200-43950200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:43933400-43948000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:43933600-43948200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:43933600-43948200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:43933600-43949800	Weak transcription	Adipose Nuclei	Adipose
13	chr10:43934200-43949200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:43936400-43950000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:43938600-43948000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:43940200-43950200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:43940400-43950200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:43940400-43950200	Weak transcription	Colonic Mucosa	Colon
19	chr10:43940800-43949600	Weak transcription	Hela-S3	cervix
20	chr10:43940800-43950600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr10:43943000-43950400	Weak transcription	Fetal Intestine Large	intestine
22	chr10:43943200-43950400	Weak transcription	Fetal Stomach	stomach
23	chr10:43943800-43947800	Enhancers	Primary B cells from peripheral blood	blood
24	chr10:43943800-43950200	Weak transcription	Fetal Intestine Small	intestine
25	chr10:43945000-43950200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:43946400-43950200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:43946400-43950600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr10:43946600-43950000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr10:43946800-43949200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr10:43946800-43950000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr10:43947000-43949200	Enhancers	Primary hematopoietic stem cells	blood
32	chr10:43947000-43950200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr10:43947200-43947800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:43947200-43947800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:43947200-43947800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr10:43947200-43947800	Enhancers	Small Intestine	intestine
37	chr10:43947200-43947800	Enhancers	HUVEC	blood vessel
38	chr10:43947200-43948000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr10:43947200-43948000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr10:43947200-43948000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:43947200-43948000	Enhancers	Fetal Muscle Leg	muscle
42	chr10:43947200-43948200	Enhancers	Spleen	Spleen
43	chr10:43947200-43948200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr10:43947200-43948800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr10:43947200-43949400	Flanking Active TSS	GM12878-XiMat	blood
46	chr10:43947200-43949800	Enhancers	Primary T cells from cord blood	blood
47	chr10:43947200-43949800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr10:43947200-43950000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:43947200-43950200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr10:43947200-43950200	Enhancers	HMEC	breast

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