Variant report

Variant	rs1861888
Chromosome Location	chr14:77763766-77763767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77618833..77620755-chr14:77763433..77765075,2	MCF-7	breast:
2	chr14:77763316..77765397-chr14:77767519..77770397,2	K562	blood:
3	chr14:77744963..77747141-chr14:77762245..77764781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10132619	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs1017186	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs1046428	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs11847091	1.00[CHD][hapmap]
rs11850308	0.86[CHB][hapmap]
rs11850771	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12894594	0.82[ASN][1000 genomes]
rs12894718	0.86[CHB][hapmap]
rs1468951	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs17105724	1.00[CHD][hapmap]
rs1861887	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2111700	0.86[CHB][hapmap]
rs2160838	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs2160839	0.81[ASN][1000 genomes]
rs2270419	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2363640	0.88[CHB][hapmap];0.86[GIH][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2364155	0.86[CHB][hapmap]
rs3209079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs3759731	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs3815625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs383064	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs4141640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs451925	0.93[CEU][hapmap];0.88[CHB][hapmap]
rs4899649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4903566	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap]
rs8014716	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9671248	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs972725	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1861888	FAM75C1	trans	lymphoblastoid	seeQTL
rs1861888	POMT2	cis	parietal	SCAN
rs1861888	ACOT4	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr14:77740200-77766800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
4	chr14:77740400-77766000	Weak transcription	Stomach Mucosa	stomach
5	chr14:77740800-77766200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
8	chr14:77742000-77766600	Strong transcription	Placenta	Placenta
9	chr14:77742200-77767600	Strong transcription	Stomach Smooth Muscle	stomach
10	chr14:77742400-77766400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:77742400-77766400	Strong transcription	Adipose Nuclei	Adipose
12	chr14:77742400-77780200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:77742600-77766600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr14:77744000-77771400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr14:77746600-77767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:77749200-77766400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:77750200-77767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:77750800-77768000	Weak transcription	K562	blood
19	chr14:77751200-77764600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr14:77751400-77769200	Weak transcription	NHLF	lung
21	chr14:77751400-77769800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr14:77751400-77775600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr14:77751400-77786200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr14:77751800-77767600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr14:77751800-77775600	Weak transcription	Thymus	Thymus
26	chr14:77752200-77775600	Weak transcription	Fetal Thymus	thymus
27	chr14:77752600-77773000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr14:77752600-77779200	Weak transcription	Fetal Heart	heart
29	chr14:77753000-77764000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr14:77753600-77771800	Weak transcription	Fetal Brain Male	brain
31	chr14:77753800-77764400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr14:77754400-77763800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr14:77754600-77769200	Weak transcription	NHDF-Ad	bronchial
34	chr14:77754600-77771000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr14:77756600-77766600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr14:77756800-77767200	Strong transcription	Fetal Muscle Leg	muscle
37	chr14:77757600-77767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:77758200-77765200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr14:77758400-77767800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr14:77759200-77765800	Weak transcription	HUVEC	blood vessel
41	chr14:77759400-77763800	Weak transcription	NH-A	brain
42	chr14:77759400-77764400	Weak transcription	Fetal Lung	lung
43	chr14:77759400-77767600	Weak transcription	Psoas Muscle	Psoas
44	chr14:77759600-77764200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:77760000-77763800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:77760000-77766400	Strong transcription	Liver	Liver
47	chr14:77760400-77764800	Weak transcription	HSMMtube	muscle
48	chr14:77760400-77773000	Strong transcription	Fetal Stomach	stomach
49	chr14:77761000-77765000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr14:77761000-77765800	Strong transcription	Brain Hippocampus Middle	brain

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