Variant report

Variant	rs9917002
Chromosome Location	chr19:42969613-42969614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42957018..42958955-chr19:42966845..42969833,2	MCF-7	breast:
2	chr19:42968131..42971103-chr19:42973928..42976779,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10401178	1.00[CEU][hapmap];0.83[AFR][1000 genomes]
rs10401428	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10402853	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10403065	0.93[AMR][1000 genomes]
rs10404589	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs10405152	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405179	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405410	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes]
rs10405891	0.81[AMR][1000 genomes]
rs10405942	0.93[AMR][1000 genomes]
rs10406227	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408822	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10412074	0.83[AFR][1000 genomes]
rs10412594	0.82[AFR][1000 genomes]
rs10414396	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414969	0.81[AMR][1000 genomes]
rs10416108	1.00[CEU][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes]
rs10416915	0.81[AMR][1000 genomes]
rs10417560	0.81[AMR][1000 genomes]
rs10418090	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10418997	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419561	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10420773	0.81[AFR][1000 genomes]
rs10422191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423227	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10424206	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10425666	0.83[AFR][1000 genomes]
rs11878959	1.00[CEU][hapmap]
rs11878991	1.00[CEU][hapmap]
rs11879033	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11880554	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs11881583	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882225	0.93[AMR][1000 genomes]
rs11882291	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11883406	1.00[CEU][hapmap]
rs11883425	1.00[CEU][hapmap]
rs13343840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345272	0.93[AMR][1000 genomes]
rs13345659	0.81[AMR][1000 genomes]
rs16975743	0.81[AMR][1000 genomes]
rs16975750	0.81[AMR][1000 genomes]
rs16975787	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975799	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975815	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975862	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2051832	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2051833	0.93[AMR][1000 genomes]
rs28403155	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28425201	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28448880	0.81[AMR][1000 genomes]
rs28473486	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28588100	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28625452	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35623577	0.81[AMR][1000 genomes]
rs41348545	0.82[AFR][1000 genomes]
rs41381546	0.83[AFR][1000 genomes]
rs41421250	0.82[AFR][1000 genomes]
rs57018456	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58050143	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58162305	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58702905	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6509015	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs6509019	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes]
rs7246161	1.00[CEU][hapmap]
rs7246591	1.00[CEU][hapmap]
rs7247278	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs7248439	0.81[AMR][1000 genomes]
rs7248907	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7249304	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252874	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253634	0.84[AFR][1000 genomes]
rs7255271	0.93[AMR][1000 genomes]
rs7256226	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7258854	1.00[CEU][hapmap]
rs7259335	0.81[AFR][1000 genomes]
rs8101378	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8104731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105525	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs8106836	0.82[AFR][1000 genomes]
rs8107720	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8108992	0.81[AFR][1000 genomes]
rs8110904	0.90[YRI][hapmap]
rs8110922	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8111171	0.82[AFR][1000 genomes]
rs9749434	0.83[AFR][1000 genomes]
rs9916999	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription 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	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42957400-42970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr19:42960000-42970200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:42960200-42970000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:42960400-42971000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:42960600-42969800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:42961000-42970200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:42961800-42970000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:42961800-42970000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:42961800-42970200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:42961800-42970200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:42961800-42970200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:42965200-42970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:42965800-42972400	Enhancers	Primary B cells from peripheral blood	blood
16	chr19:42966400-42970000	Weak transcription	Left Ventricle	heart
17	chr19:42966600-42970000	Weak transcription	Adipose Nuclei	Adipose
18	chr19:42966600-42970000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:42966600-42970400	Weak transcription	Stomach Mucosa	stomach
20	chr19:42966800-42970200	Weak transcription	Right Atrium	heart
21	chr19:42967000-42970000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:42967000-42970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:42967200-42970200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:42967200-42970400	Weak transcription	Fetal Intestine Large	intestine
25	chr19:42967200-42970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:42967200-42972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:42967200-42972400	Weak transcription	Esophagus	oesophagus
28	chr19:42967400-42970200	Weak transcription	Brain Anterior Caudate	brain
29	chr19:42967400-42970800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:42967400-42972400	Weak transcription	Fetal Intestine Small	intestine
31	chr19:42967600-42970200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:42967600-42970200	Weak transcription	Brain Angular Gyrus	brain
33	chr19:42967600-42970200	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:42968200-42970200	Weak transcription	Brain Substantia Nigra	brain
35	chr19:42968200-42970200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:42968400-42970000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:42969000-42972200	Enhancers	Primary B cells from cord blood	blood
38	chr19:42969200-42971000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:42969400-42971400	Flanking Active TSS	GM12878-XiMat	blood
40	chr19:42969400-42972000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr19:42969400-42973000	Enhancers	HepG2	liver
42	chr19:42969400-42975200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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