Variant report

Variant	rs872106
Chromosome Location	chr10:99236217-99236218
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99235824..99238488-chr10:99250423..99252230,2	MCF-7	breast:
2	chr10:99233786..99237175-chr10:99256674..99259199,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165886	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10786352	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10882947	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882950	0.81[CHD][hapmap]
rs10882951	0.81[CHD][hapmap]
rs10882953	0.81[CEU][hapmap]
rs11189247	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11591644	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11592144	0.81[CEU][hapmap];0.89[CHD][hapmap]
rs11592973	1.00[ASW][hapmap];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];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11593116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11595151	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11598766	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812581	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12767191	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29001259	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs29001262	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29001311	1.00[JPT][hapmap]
rs29001315	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34041345	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34312169	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs34452362	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34759540	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584123	1.00[CHB][hapmap]
rs7073097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7077917	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090595	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7090757	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7901283	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs872106	RRP12	cis	cerebellum	SCAN
rs872106	SCD	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99210000-99243800	Strong transcription	Primary T cells from cord blood	blood
2	chr10:99210000-99243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:99210000-99244000	Strong transcription	Fetal Stomach	stomach
4	chr10:99210000-99244200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:99210200-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:99210400-99243600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr10:99210400-99244800	Strong transcription	Fetal Thymus	thymus
8	chr10:99210600-99238800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:99210600-99239000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:99210600-99241800	Strong transcription	Thymus	Thymus
11	chr10:99210600-99243800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr10:99210600-99244200	Strong transcription	Placenta	Placenta
13	chr10:99210800-99239000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr10:99210800-99243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:99210800-99244000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:99210800-99246000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr10:99211000-99238800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:99211000-99243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:99211000-99246400	Strong transcription	Dnd41	blood
20	chr10:99211200-99244800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:99211200-99246200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr10:99211200-99246600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:99211400-99239000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr10:99211400-99241600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr10:99211600-99239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:99211800-99241200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr10:99214400-99242000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr10:99214400-99246400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:99214600-99242800	Strong transcription	Fetal Muscle Leg	muscle
30	chr10:99214600-99243800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:99214600-99243800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr10:99214800-99243800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:99215000-99238000	Strong transcription	Fetal Lung	lung
34	chr10:99215200-99242400	Strong transcription	Left Ventricle	heart
35	chr10:99215200-99243800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:99215400-99243800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr10:99215400-99254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:99216800-99243800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:99217200-99237200	Weak transcription	Fetal Heart	heart
40	chr10:99217800-99242000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr10:99218200-99244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:99224200-99245000	Strong transcription	Fetal Intestine Small	intestine
43	chr10:99224400-99244800	Strong transcription	Fetal Intestine Large	intestine
44	chr10:99225000-99240400	Strong transcription	A549	lung
45	chr10:99225400-99242000	Strong transcription	Brain Substantia Nigra	brain
46	chr10:99225600-99238800	Strong transcription	HepG2	liver
47	chr10:99227600-99238000	Strong transcription	Hela-S3	cervix
48	chr10:99227600-99246600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:99228200-99240400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr10:99229200-99238800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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