Variant report

Variant	rs12709849
Chromosome Location	chr19:41918355-41918356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41917692..41920581-chr19:41927683..41929830,2	K562	blood:
2	chr19:41917932..41920141-chr19:41945281..41947349,2	K562	blood:
3	chr19:41911962..41915322-chr19:41916825..41920523,3	K562	blood:
4	chr19:41917692..41924780-chr19:41925842..41930089,8	K562	blood:
5	chr19:41917342..41919292-chr19:41920976..41923914,2	K562	blood:
6	chr19:41903791..41906982-chr19:41915611..41919642,3	K562	blood:
7	chr19:41913001..41915565-chr19:41918235..41920074,2	K562	blood:

Variant related genes	Relation type
ENSG00000268987	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000105341	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10409485	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10413735	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10416743	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10417311	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10417997	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420556	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10422783	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422956	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10432268	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1043413	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1077856	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853751	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083618	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083619	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667848	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11667908	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668924	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11670583	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670668	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670725	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11670757	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11880539	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11883104	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12980966	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12982607	0.81[ASN][1000 genomes]
rs13344547	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13344563	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13345590	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13346603	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473248	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166925	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16975238	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17318596	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17318666	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1967333	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1967334	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2231940	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241706	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241707	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241708	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241709	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241710	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241711	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304242	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2317131	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2569400	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2569754	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284648	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284649	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284650	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284651	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284652	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284654	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284655	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284656	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284657	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284658	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284660	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284661	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284662	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs284663	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3213860	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213861	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745290	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745292	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3786553	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810174	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810175	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826713	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4605279	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4674	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802116	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802117	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802118	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803461	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803462	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803463	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803465	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803467	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803468	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803469	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55986560	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58961854	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62117461	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62117462	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6508977	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247332	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255918	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7258973	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103531	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8105833	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs878082	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs878083	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892044	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304593	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12709849	CTC-435M10.6	cis	Whole Blood	GTEx
rs12709849	B3GNT8	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41904600-41924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:41905000-41924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:41905000-41930800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:41905200-41926600	Weak transcription	Small Intestine	intestine
5	chr19:41913600-41925800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr19:41913800-41919400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:41913800-41919600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:41913800-41921000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:41913800-41927000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:41913800-41932600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:41914600-41918800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:41915200-41918800	Weak transcription	Fetal Brain Male	brain
13	chr19:41915200-41932600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:41915400-41932800	Weak transcription	Hela-S3	cervix
15	chr19:41915600-41932800	Weak transcription	NH-A	brain
16	chr19:41915800-41920200	Weak transcription	A549	lung
17	chr19:41916000-41918400	Enhancers	Psoas Muscle	Psoas
18	chr19:41916000-41919000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:41916000-41924200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:41916000-41932000	Strong transcription	Fetal Stomach	stomach
21	chr19:41916000-41932400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:41916200-41919000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:41916200-41919600	Strong transcription	Fetal Intestine Small	intestine
24	chr19:41916200-41921600	Strong transcription	NHLF	lung
25	chr19:41916200-41922200	Weak transcription	Osteobl	bone
26	chr19:41916200-41926200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:41916200-41927000	Strong transcription	Placenta	Placenta
28	chr19:41916200-41928000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:41916200-41932000	Weak transcription	HUVEC	blood vessel
30	chr19:41916400-41918600	Genic enhancers	Left Ventricle	heart
31	chr19:41916400-41918800	Weak transcription	HepG2	liver
32	chr19:41916400-41919000	Strong transcription	Spleen	Spleen
33	chr19:41916400-41919400	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:41916400-41919600	Strong transcription	Fetal Intestine Large	intestine
35	chr19:41916400-41920200	Weak transcription	HSMM	muscle
36	chr19:41916400-41920400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:41916400-41920800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr19:41916400-41921200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:41916400-41922800	Weak transcription	Fetal Kidney	kidney
40	chr19:41916400-41925000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr19:41916400-41925200	Strong transcription	Liver	Liver
42	chr19:41916400-41928400	Weak transcription	K562	blood
43	chr19:41916400-41930800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:41916400-41931600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:41916400-41932000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:41916400-41932600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr19:41916400-41932800	Strong transcription	Brain Germinal Matrix	brain
48	chr19:41916400-41932800	Strong transcription	Fetal Brain Female	brain
49	chr19:41916400-41933000	Strong transcription	Thymus	Thymus
50	chr19:41916600-41920400	Strong transcription	Gastric	stomach

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