Variant report

Variant	rs16975238
Chromosome Location	chr19:41944985-41944986
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr19:41944818-41945054	SH-SY5Y	brain:	n/a	n/a
2	REST	chr19:41944925-41946245	H1-neurons	neurons:	n/a	n/a
3	HCFC1	chr19:41944890-41946158	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr19:41944770-41947242	A549	lung:	n/a	chr19:41945823-41945836

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41944180..41946970-chr7:80547778..80549990,2	MCF-7	breast:
2	chr19:41857565..41861683-chr19:41942530..41947234,4	MCF-7	breast:
3	chr19:41859512..41861303-chr19:41943975..41945825,3	K562	blood:
4	chr19:41944238..41947062-chr19:41948910..41951983,5	K562	blood:
5	chr19:41930070..41932098-chr19:41944342..41947114,3	K562	blood:
6	chr19:41931962..41935414-chr19:41944317..41947167,6	MCF-7	breast:
7	chr19:41868336..41870018-chr19:41944233..41946275,2	K562	blood:
8	chr19:41944280..41946189-chr19:42004239..42006678,2	K562	blood:
9	chr19:41932975..41939032-chr19:41942824..41947362,11	K562	blood:
10	chr19:41940773..41942496-chr19:41944318..41947193,2	MCF-7	breast:
11	chr19:41901938..41905441-chr19:41944047..41947443,5	K562	blood:
12	chr19:41868336..41871272-chr19:41944233..41948538,5	K562	blood:
13	chr19:41944614..41946975-chr19:41948804..41950642,2	MCF-7	breast:

No data

Variant related genes	Relation type
C19orf69	TF binding region
ATP5SL	TF binding region
ENSG00000142046	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000204978	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000268475	Chromatin interaction
ENSG00000267107	Chromatin interaction
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10409485	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10413735	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10416743	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10417311	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10417997	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10420556	0.84[EUR][1000 genomes]
rs10422783	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10422956	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10432268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1043413	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1077856	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10853751	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11083618	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083619	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11667848	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11667908	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11668924	0.82[EUR][1000 genomes]
rs11670583	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11670668	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11670725	0.84[EUR][1000 genomes]
rs11670757	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11880539	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11883104	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12602	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs12709849	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13344547	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13344563	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13345590	0.84[EUR][1000 genomes]
rs13346603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473248	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs166925	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17318596	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17318666	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967333	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967334	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2231940	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241706	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241707	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241708	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241709	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241710	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241711	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288871	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304242	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317131	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2569400	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2569754	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284648	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284649	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284650	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284651	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs284652	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs284654	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs284655	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs284656	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs284657	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284658	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284660	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284661	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284662	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284663	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3213860	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3213861	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3745290	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3745292	0.83[EUR][1000 genomes]
rs3786553	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3816037	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3826713	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4605279	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs4674	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802116	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802117	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802118	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803461	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803462	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803463	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803465	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803467	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803468	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803469	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55986560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58961854	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62117461	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62117462	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508977	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7247332	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7258973	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8103531	0.84[EUR][1000 genomes]
rs8105833	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs878082	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs878083	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs892044	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs9304593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16975238	B3GNT8	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41934400-41945000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:41934800-41945400	Weak transcription	Small Intestine	intestine
3	chr19:41935000-41945000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:41938600-41945000	Weak transcription	HSMMtube	muscle
5	chr19:41938800-41945000	Weak transcription	Fetal Kidney	kidney
6	chr19:41938800-41945000	Weak transcription	NHDF-Ad	bronchial
7	chr19:41938800-41945200	Weak transcription	Right Atrium	heart
8	chr19:41939000-41945000	Weak transcription	Primary B cells from cord blood	blood
9	chr19:41939200-41945000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:41939200-41945000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:41939400-41945000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:41939400-41945000	Weak transcription	Stomach Mucosa	stomach
13	chr19:41939400-41945200	Weak transcription	Colonic Mucosa	Colon
14	chr19:41939600-41945000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:41939600-41945200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:41939600-41945200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:41939600-41945400	Weak transcription	Gastric	stomach
18	chr19:41942400-41945200	Weak transcription	Aorta	Aorta
19	chr19:41942600-41945000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:41942800-41945000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr19:41942800-41945200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:41943000-41945000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:41943000-41945000	Weak transcription	Brain Anterior Caudate	brain
24	chr19:41943000-41945000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:41943000-41945000	Weak transcription	Brain Substantia Nigra	brain
26	chr19:41943000-41945400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:41943800-41945200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr19:41944000-41945000	Weak transcription	Osteobl	bone
29	chr19:41944000-41945200	Weak transcription	Ovary	ovary
30	chr19:41944200-41945000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:41944200-41945000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr19:41944200-41945000	Enhancers	Primary hematopoietic stem cells	blood
33	chr19:41944200-41945000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:41944200-41945000	Weak transcription	Adipose Nuclei	Adipose
35	chr19:41944200-41945000	Enhancers	Fetal Brain Male	brain
36	chr19:41944200-41945200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr19:41944200-41945200	Weak transcription	Placenta	Placenta
38	chr19:41944200-41945200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr19:41944200-41945400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:41944400-41945000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr19:41944400-41945000	Enhancers	Primary T cells from cord blood	blood
42	chr19:41944400-41945000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:41944400-41945000	Enhancers	Fetal Intestine Small	intestine
44	chr19:41944400-41945000	Enhancers	Right Ventricle	heart
45	chr19:41944400-41945200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:41944400-41945200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:41944400-41945200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:41944400-41945200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:41944400-41945200	Enhancers	Brain Hippocampus Middle	brain
50	chr19:41944400-41945200	Enhancers	Fetal Heart	heart

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