Variant report

Variant	rs4808906
Chromosome Location	chr19:19133163-19133164
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19093006..19095343-chr19:19131973..19134830,2	K562	blood:
2	chr19:19131657..19133627-chr19:19143750..19145412,2	K562	blood:
3	chr19:19131657..19140875-chr19:19141068..19145619,15	K562	blood:
4	chr19:19132088..19135001-chr19:19135868..19138167,2	MCF-7	breast:
5	chr19:19125900..19131875-chr19:19132072..19136394,7	K562	blood:

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1007483	1.00[JPT][hapmap]
rs10221504	0.94[ASN][1000 genomes]
rs10403222	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10404627	0.94[ASN][1000 genomes]
rs10405189	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405635	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10409164	0.94[ASN][1000 genomes]
rs10410451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10410568	0.94[ASN][1000 genomes]
rs10414676	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10416783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417974	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10422335	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10422906	0.94[ASN][1000 genomes]
rs10423742	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10423815	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1079543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10854005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1124921	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666120	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11670204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670239	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11671696	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11878368	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975676	0.94[ASN][1000 genomes]
rs12975754	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12976302	0.91[ASN][1000 genomes]
rs12978822	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12979565	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982014	0.87[AMR][1000 genomes]
rs12985799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1859267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2107263	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158320	0.98[ASN][1000 genomes]
rs2240094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240095	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2269869	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs2285851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2313736	0.95[ASN][1000 genomes]
rs2872394	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3180770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808172	0.85[CEU][hapmap]
rs4808179	0.98[ASN][1000 genomes]
rs4808184	0.94[ASN][1000 genomes]
rs4808900	0.81[AMR][1000 genomes]
rs4808902	0.95[ASN][1000 genomes]
rs4808904	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808905	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808907	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808911	0.98[ASN][1000 genomes]
rs4808913	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808916	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6511010	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511011	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511014	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511015	0.98[ASN][1000 genomes]
rs6511017	0.98[ASN][1000 genomes]
rs6511018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6511021	0.85[CHB][hapmap]
rs7248399	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7248771	0.94[ASN][1000 genomes]
rs7250131	0.94[ASN][1000 genomes]
rs7253244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255937	0.94[ASN][1000 genomes]
rs7256648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7257635	0.90[ASN][1000 genomes]
rs7258637	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259510	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs757220	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8101529	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103431	0.94[ASN][1000 genomes]
rs8104799	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106146	0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107710	0.88[ASN][1000 genomes]
rs8109654	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110629	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112566	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs916898	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929215	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304959	0.98[ASN][1000 genomes]
rs9676917	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4808906	TMEM161A	cis	Muscle Skeletal	GTEx
rs4808906	SFRS14	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
6	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
9	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:19110600-19142400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:19111000-19133600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:19123600-19133600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr19:19124000-19133400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:19124600-19133200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:19126400-19143400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:19126600-19137600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:19126800-19142600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:19127000-19133200	Strong transcription	Thymus	Thymus
22	chr19:19127800-19133200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:19127800-19135200	Weak transcription	Psoas Muscle	Psoas
24	chr19:19128000-19142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:19128000-19142800	Strong transcription	Fetal Intestine Small	intestine
26	chr19:19128000-19142800	Weak transcription	Stomach Mucosa	stomach
27	chr19:19128400-19136200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:19129800-19133200	Weak transcription	Fetal Brain Male	brain
29	chr19:19130200-19133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:19130200-19133200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:19130200-19133200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:19130200-19133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:19130200-19133200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:19130200-19133200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:19130200-19133200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:19130200-19133200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:19130200-19133200	Weak transcription	Aorta	Aorta
38	chr19:19130200-19133200	Weak transcription	Placenta	Placenta
39	chr19:19130200-19133200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:19130200-19133200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr19:19130200-19133200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:19130200-19133200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:19130200-19133200	Weak transcription	Small Intestine	intestine
44	chr19:19130200-19133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:19130200-19133400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr19:19130200-19133400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:19130200-19133400	Weak transcription	Colonic Mucosa	Colon
48	chr19:19130200-19135000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:19130200-19136200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:19130200-19141800	Weak transcription	Fetal Heart	heart

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