Variant report

Variant	rs12249534
Chromosome Location	chr10:27805358-27805359
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27793437..27795941-chr10:27804290..27806417,2	K562	blood:
2	chr10:27803807..27806006-chr10:27825397..27828002,2	MCF-7	breast:
3	chr10:27802552..27806516-chr10:27806924..27811120,4	K562	blood:
4	chr10:27804368..27807313-chr10:27807904..27811120,3	K562	blood:
5	chr10:27802914..27806574-chr10:27810162..27816250,5	MCF-7	breast:
6	chr10:27803692..27805636-chr10:27811125..27812771,2	K562	blood:
7	chr10:27804136..27807290-chr10:27811271..27813814,3	K562	blood:

Variant related genes	Relation type
ENSG00000099246	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10437434	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10508723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10764699	0.86[AFR][1000 genomes]
rs11015830	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015838	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015842	0.91[AFR][1000 genomes]
rs11015844	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015853	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12242968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12248740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12254670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12258435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261373	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261690	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12263216	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12267298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2368234	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59498921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60909738	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61486615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9651381	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers 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 target site	27 gene(s)	inside rSNPs	diseases
3	nsv1045257	chr10:27572440-27926946	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1053952	chr10:27659365-27915029	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27794200-27806800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:27794200-27817000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:27794400-27824000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr10:27794400-27837400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:27794800-27814200	Weak transcription	Ovary	ovary
6	chr10:27794800-27814600	Weak transcription	HSMMtube	muscle
7	chr10:27794800-27822800	Weak transcription	Colonic Mucosa	Colon
8	chr10:27794800-27823200	Weak transcription	Esophagus	oesophagus
9	chr10:27794800-27823200	Weak transcription	Spleen	Spleen
10	chr10:27795000-27806000	Weak transcription	Fetal Kidney	kidney
11	chr10:27795000-27813000	Weak transcription	Right Atrium	heart
12	chr10:27795200-27813800	Weak transcription	Fetal Brain Male	brain
13	chr10:27795200-27816800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:27795600-27814800	Weak transcription	Pancreas	Pancrea
15	chr10:27795600-27816800	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:27795800-27822600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:27795800-27832600	Weak transcription	Small Intestine	intestine
18	chr10:27796000-27814600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr10:27798400-27805800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr10:27798400-27807600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:27799400-27811200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:27799600-27813800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr10:27800200-27805600	Strong transcription	Fetal Stomach	stomach
24	chr10:27800400-27806200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:27800800-27823200	Weak transcription	Brain Anterior Caudate	brain
26	chr10:27801000-27812200	Weak transcription	K562	blood
27	chr10:27801000-27813400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:27801000-27813600	Weak transcription	Psoas Muscle	Psoas
29	chr10:27801000-27815200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr10:27801000-27816600	Weak transcription	HUVEC	blood vessel
31	chr10:27801200-27813400	Weak transcription	Brain Germinal Matrix	brain
32	chr10:27801400-27810600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:27801600-27813800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:27801800-27829000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr10:27802200-27805800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr10:27802200-27805800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr10:27802800-27813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:27803000-27806000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr10:27803000-27813000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:27803000-27813600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:27803200-27806200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:27803200-27806400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:27803200-27810400	Weak transcription	GM12878-XiMat	blood
44	chr10:27803200-27812600	Weak transcription	Fetal Lung	lung
45	chr10:27803200-27818200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr10:27803200-27822600	Weak transcription	NH-A	brain
47	chr10:27803400-27814000	Weak transcription	A549	lung
48	chr10:27803400-27814200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr10:27803400-27822400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:27803400-27823200	Weak transcription	Fetal Muscle Trunk	muscle

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