Variant report

Variant	rs8105642
Chromosome Location	chr19:19558468-19558469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19521179..19523703-chr19:19556987..19559661,2	MCF-7	breast:
2	chr19:19555793..19560034-chr19:19567038..19569672,4	MCF-7	breast:
3	chr19:19497521..19500034-chr19:19556713..19558858,2	K562	blood:
4	chr19:19517137..19518642-chr19:19558154..19560322,2	K562	blood:
5	chr19:19558288..19561213-chr19:19569114..19571346,2	K562	blood:
6	chr19:19517059..19519979-chr19:19556271..19558619,2	MCF-7	breast:
7	chr19:19515791..19518099-chr19:19558390..19560327,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10406278	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10407933	0.82[CEU][hapmap]
rs10423874	0.87[CEU][hapmap]
rs1064395	0.81[CEU][hapmap]
rs11085264	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11555053	0.81[CEU][hapmap]
rs11668203	1.00[EUR][1000 genomes]
rs11669558	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11669730	0.88[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670687	0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670761	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670775	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs11671253	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529745	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1560687	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17216041	0.81[CEU][hapmap]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751061	0.88[CEU][hapmap]
rs2010506	0.89[YRI][hapmap]
rs2011503	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs2060274	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2860494	0.82[EUR][1000 genomes]
rs2905429	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905433	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905434	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2916070	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916072	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2916075	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965178	0.83[EUR][1000 genomes]
rs2965179	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965181	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965184	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2965186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2965187	0.86[AFR][1000 genomes]
rs2965190	0.83[CEU][hapmap]
rs2965195	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2965201	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34487417	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34667451	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45556231	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45631651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808204	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808205	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808206	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808934	0.81[CEU][hapmap]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808958	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808968	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808969	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808970	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55927782	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56280531	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56291054	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56330647	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58074958	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61744761	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511027	0.81[CEU][hapmap]
rs6511029	0.81[EUR][1000 genomes]
rs7245689	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7250233	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs7256028	0.90[EUR][1000 genomes]
rs751857	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs754256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs8100927	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101219	0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111093	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs998732	0.81[CEU][hapmap]

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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8105642	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19540200-19562600	Weak transcription	Fetal Intestine Large	intestine
3	chr19:19544400-19563400	Weak transcription	Fetal Kidney	kidney
4	chr19:19545400-19562200	Weak transcription	Brain Angular Gyrus	brain
5	chr19:19545600-19568600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:19545800-19563400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:19545800-19568600	Weak transcription	Brain Substantia Nigra	brain
8	chr19:19545800-19570600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:19546000-19558600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr19:19546000-19566600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:19546200-19569000	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:19550000-19562200	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:19550400-19562400	Weak transcription	A549	lung
14	chr19:19551000-19571200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:19553000-19563000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr19:19553400-19562200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr19:19553400-19564400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:19553400-19564800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:19553600-19558600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:19553800-19560200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:19554000-19558800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:19554000-19559200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:19554000-19560000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr19:19554000-19564000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:19554200-19559000	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:19554200-19564600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr19:19554400-19558800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr19:19554600-19559800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr19:19554800-19560000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:19555000-19559000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr19:19555000-19559000	Enhancers	Stomach Mucosa	stomach
32	chr19:19555000-19559000	Enhancers	NHDF-Ad	bronchial
33	chr19:19555000-19559200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:19555000-19559400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:19555200-19558600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:19555200-19559000	Enhancers	NHLF	lung
37	chr19:19555200-19565800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19555400-19558600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:19555400-19558800	Enhancers	Small Intestine	intestine
40	chr19:19555400-19559000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr19:19555400-19559000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr19:19555400-19559000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr19:19555400-19559000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr19:19555400-19559400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr19:19555800-19559000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:19556000-19562000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr19:19556000-19562000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:19556000-19567400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:19556200-19563000	Weak transcription	Aorta	Aorta
50	chr19:19556200-19567400	Weak transcription	Osteobl	bone

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