Variant report

Variant	rs1555944
Chromosome Location	chr14:68625118-68625119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68624416..68626843-chr14:69258780..69260587,2	MCF-7	breast:
2	chr14:68624965..68627608-chr14:68656572..68658244,2	MCF-7	breast:
3	chr14:68619639..68622771-chr14:68624194..68627478,3	MCF-7	breast:
4	chr14:68624109..68626673-chr14:69260715..69262664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1022978	0.90[EUR][1000 genomes]
rs11846526	0.90[YRI][hapmap]
rs12437043	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1274656	0.80[CEU][hapmap]
rs12880237	0.85[ASW][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs12894297	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1467673	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1555945	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17104908	0.84[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes]
rs17105269	0.91[YRI][hapmap]
rs1952245	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs1952246	0.94[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs1958111	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs1958112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1958113	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1958115	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs1958116	1.00[CEU][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1980850	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2038979	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2243905	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2254173	0.85[EUR][1000 genomes]
rs2478777	0.90[EUR][1000 genomes]
rs2588806	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2588807	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2588808	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2588809	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs2588813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588814	0.94[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs2588815	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2588816	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2588818	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2588819	0.94[CEU][hapmap];0.93[GIH][hapmap];0.87[EUR][1000 genomes]
rs2588820	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2588821	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2588823	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2588824	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2588825	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2588826	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2588827	0.94[CEU][hapmap];0.81[GIH][hapmap];0.85[EUR][1000 genomes]
rs2588828	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2588829	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2588830	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2588831	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2588832	0.83[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs2588833	0.84[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes]
rs2588834	0.84[CEU][hapmap]
rs2588835	0.86[AMR][1000 genomes]
rs2767366	0.83[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2767367	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2767368	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2767377	0.83[AMR][1000 genomes]
rs2767379	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2767382	0.86[EUR][1000 genomes]
rs2767383	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2767384	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs365934	0.84[AMR][1000 genomes]
rs372143	0.84[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes]
rs373918	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs378408	0.84[AMR][1000 genomes]
rs401021	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs411547	0.84[CEU][hapmap];0.84[AMR][1000 genomes]
rs424032	0.87[AMR][1000 genomes]
rs431649	0.84[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes]
rs435620	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs437585	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs448445	0.84[CEU][hapmap]
rs6573817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7141160	0.84[CEU][hapmap]
rs7141450	0.82[CEU][hapmap]
rs7156822	0.87[AMR][1000 genomes]
rs8011527	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959039	0.89[EUR][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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1048794	chr14:68614152-68649231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555944	GALNTL1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68612600-68628000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr14:68613000-68631200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr14:68620800-68627000	Weak transcription	Psoas Muscle	Psoas
4	chr14:68621200-68630000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:68621400-68628200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr14:68621400-68631000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr14:68622400-68625600	Enhancers	Liver	Liver
8	chr14:68622400-68625600	Enhancers	Rectal Smooth Muscle	rectum
9	chr14:68622400-68625800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr14:68622800-68625600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:68622800-68625600	Weak transcription	Fetal Stomach	stomach
12	chr14:68623000-68625400	Enhancers	Colon Smooth Muscle	Colon
13	chr14:68623000-68625600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:68623000-68627400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:68623000-68630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:68623000-68631000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr14:68623200-68627000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:68623200-68627400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr14:68623200-68627400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:68623800-68625600	Enhancers	Hela-S3	cervix
21	chr14:68624000-68630400	Weak transcription	Ovary	ovary
22	chr14:68624200-68625200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr14:68624200-68625200	Enhancers	NHDF-Ad	bronchial
24	chr14:68624200-68625400	Enhancers	Fetal Intestine Large	intestine
25	chr14:68624200-68625600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr14:68624200-68625600	Enhancers	HMEC	breast
27	chr14:68624200-68625800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:68624200-68626000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:68624400-68625200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:68624400-68625200	Enhancers	Fetal Lung	lung
31	chr14:68624400-68625600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:68624600-68625200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr14:68624600-68625200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr14:68624600-68625200	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr14:68624600-68625200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr14:68624600-68625200	Enhancers	HSMMtube	muscle
37	chr14:68624600-68625200	Enhancers	Osteobl	bone
38	chr14:68624600-68625400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr14:68624600-68625400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:68624600-68625600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr14:68624600-68625600	Enhancers	HepG2	liver
42	chr14:68624600-68625800	Enhancers	Adipose Nuclei	Adipose
43	chr14:68624800-68625200	Enhancers	Stomach Smooth Muscle	stomach
44	chr14:68624800-68625400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr14:68624800-68625400	Enhancers	Primary hematopoietic stem cells	blood
46	chr14:68624800-68625600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr14:68624800-68628000	Enhancers	A549	lung
48	chr14:68625000-68625200	Flanking Active TSS	NHEK	skin
49	chr14:68625000-68626800	Enhancers	Fetal Kidney	kidney
50	chr14:68625000-68627600	Weak transcription	Stomach Mucosa	stomach

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