Variant report

Variant	rs16875618
Chromosome Location	chr5:5484080-5484081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:5481130..5482758-chr5:5483384..5486103,2	MCF-7	breast:
2	chr5:5472240..5473764-chr5:5482483..5484530,2	K562	blood:
3	chr5:5483935..5486705-chr5:6402529..6404971,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10462631	1.00[EUR][1000 genomes]
rs1473230	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs16875584	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16875589	0.81[EUR][1000 genomes]
rs16875590	0.81[EUR][1000 genomes]
rs16875597	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16875609	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs16875617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16875619	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16900246	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16900247	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306349	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs35190184	0.95[EUR][1000 genomes]
rs3747730	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[ASN][1000 genomes]
rs3806873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4283757	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs4702268	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4702269	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4702270	1.00[EUR][1000 genomes]
rs4702271	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59189910	0.85[AMR][1000 genomes]
rs6874736	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs72646678	1.00[EUR][1000 genomes]
rs728079	0.86[EUR][1000 genomes]
rs73736664	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713294	0.91[EUR][1000 genomes]
rs7713609	0.81[EUR][1000 genomes]
rs7714569	1.00[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	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16875618	GUCA1C	trans	brain	seeQTL
rs16875618	TTR	trans	brain	seeQTL
rs16875618	SH2D2A	trans	brain	seeQTL
rs16875618	LRTM1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:5458600-5495000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:5462400-5494600	Weak transcription	Colonic Mucosa	Colon
4	chr5:5463000-5493800	Weak transcription	Fetal Heart	heart
5	chr5:5465200-5493800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:5465200-5495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:5467600-5488800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:5468000-5494000	Weak transcription	Fetal Brain Male	brain
9	chr5:5470400-5492600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:5472800-5490600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:5475400-5487000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:5475400-5492400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:5475400-5494000	Weak transcription	Fetal Intestine Small	intestine
14	chr5:5475400-5495000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:5476000-5487200	Weak transcription	HSMMtube	muscle
16	chr5:5476000-5490000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:5476000-5490800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:5476200-5488000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:5476600-5484800	Weak transcription	Primary B cells from cord blood	blood
20	chr5:5476800-5486000	Weak transcription	HMEC	breast
21	chr5:5476800-5487000	Weak transcription	Brain Anterior Caudate	brain
22	chr5:5476800-5487000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:5476800-5492600	Weak transcription	A549	lung
24	chr5:5477000-5484200	Weak transcription	Osteobl	bone
25	chr5:5477000-5484800	Weak transcription	Aorta	Aorta
26	chr5:5477000-5484800	Weak transcription	HUVEC	blood vessel
27	chr5:5477000-5486200	Weak transcription	Pancreas	Pancrea
28	chr5:5477000-5486600	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:5477000-5486800	Weak transcription	Fetal Stomach	stomach
30	chr5:5477000-5487000	Weak transcription	Fetal Brain Female	brain
31	chr5:5477000-5487200	Weak transcription	Spleen	Spleen
32	chr5:5477000-5487400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:5477000-5490800	Weak transcription	Esophagus	oesophagus
34	chr5:5477000-5492600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:5477000-5494000	Weak transcription	Psoas Muscle	Psoas
36	chr5:5477000-5494200	Weak transcription	Fetal Kidney	kidney
37	chr5:5477000-5494400	Weak transcription	Small Intestine	intestine
38	chr5:5477000-5494400	Weak transcription	NHLF	lung
39	chr5:5477000-5494600	Weak transcription	Right Ventricle	heart
40	chr5:5477200-5486600	Weak transcription	Fetal Thymus	thymus
41	chr5:5477200-5493800	Weak transcription	NHDF-Ad	bronchial
42	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
43	chr5:5477400-5487800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:5477600-5486800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr5:5478200-5486000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:5478200-5486400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:5478200-5486800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:5478200-5487000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:5478200-5487200	Weak transcription	Left Ventricle	heart
50	chr5:5478400-5484800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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