Variant report

Variant	rs4917772
Chromosome Location	chr10:99249505-99249506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99248992..99255448-chr10:99256116..99258644,11	K562	blood:
2	chr10:99248310..99253998-chr10:99255944..99258497,7	MCF-7	breast:
3	chr10:99248971..99251809-chr10:99252643..99255193,3	K562	blood:

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10786350	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10786351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10882936	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882940	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882943	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10882944	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189233	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189238	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11189244	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs17112814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2275583	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29001322	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59554205	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7084687	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72833970	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7893335	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7915501	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4917772	MMS19	cis	parietal	SCAN
rs4917772	MMS19	cis	cerebellum	SCAN
rs4917772	RRP12	cis	cerebellum	SCAN
rs4917772	RRP12	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99215400-99254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:99230800-99250400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:99237200-99254800	Weak transcription	Small Intestine	intestine
4	chr10:99238000-99250200	Weak transcription	Fetal Brain Male	brain
5	chr10:99238200-99249800	Weak transcription	Psoas Muscle	Psoas
6	chr10:99239200-99254600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr10:99239400-99257400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:99239600-99250400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:99240800-99254600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:99240800-99256000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:99240800-99257400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:99241000-99250200	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:99241000-99250600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr10:99241000-99254600	Weak transcription	K562	blood
15	chr10:99241200-99250000	Weak transcription	HSMMtube	muscle
16	chr10:99241200-99250400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:99241200-99250400	Weak transcription	Fetal Lung	lung
18	chr10:99241200-99250400	Weak transcription	Gastric	stomach
19	chr10:99241200-99250400	Weak transcription	Ovary	ovary
20	chr10:99241200-99253600	Weak transcription	Fetal Kidney	kidney
21	chr10:99241200-99254600	Weak transcription	Esophagus	oesophagus
22	chr10:99241200-99254800	Weak transcription	Stomach Mucosa	stomach
23	chr10:99241200-99256800	Weak transcription	Colonic Mucosa	Colon
24	chr10:99241200-99256800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr10:99241400-99250400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:99241400-99250400	Weak transcription	Aorta	Aorta
27	chr10:99241400-99254200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:99241800-99252800	Weak transcription	Lung	lung
29	chr10:99241800-99256400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:99242000-99250400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:99242200-99250200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr10:99242200-99252600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:99242400-99250200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:99243600-99250200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:99243600-99250600	Weak transcription	Liver	Liver
36	chr10:99243800-99249600	Weak transcription	Brain Germinal Matrix	brain
37	chr10:99243800-99249800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:99243800-99249800	Weak transcription	Left Ventricle	heart
39	chr10:99243800-99250000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr10:99243800-99250200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:99243800-99250200	Weak transcription	Adipose Nuclei	Adipose
42	chr10:99243800-99250200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr10:99243800-99250200	Weak transcription	HSMM	muscle
44	chr10:99243800-99250400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr10:99243800-99250400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr10:99243800-99250400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:99243800-99250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:99243800-99250400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:99243800-99250400	Weak transcription	Pancreas	Pancrea
50	chr10:99243800-99250400	Weak transcription	Right Atrium	heart

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