Variant report

Variant	rs16846561
Chromosome Location	chr1:173869111-173869112
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173859716..173863027-chr1:173865455..173870785,5	K562	blood:
2	chr1:173865468..173869830-chr1:173871500..173875883,4	MCF-7	breast:
3	chr1:173868345..173870292-chr1:173879579..173881405,2	K562	blood:
4	chr1:173868704..173870321-chr1:173875152..173876806,2	K562	blood:
5	chr1:173813848..173815354-chr1:173868655..173871235,2	MCF-7	breast:
6	chr1:173865064..173869391-chr1:173883979..173888192,4	MCF-7	breast:
7	chr1:173805772..173808648-chr1:173867420..173869659,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117601	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs14262	0.88[LWK][hapmap];0.80[YRI][hapmap]
rs16846418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846433	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846478	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846546	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[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846593	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846660	0.80[LWK][hapmap]
rs1885679	0.86[LWK][hapmap];0.80[YRI][hapmap]
rs2065170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146372	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227617	0.88[LWK][hapmap];0.80[YRI][hapmap]
rs2235095	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2759328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57022387	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58994962	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61262741	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61649485	0.84[ASN][1000 genomes]
rs6656255	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685043	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs6687429	0.80[LWK][hapmap]
rs6691053	0.82[CHB][hapmap];0.80[LWK][hapmap]
rs6696381	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941987	0.87[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs941988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970048	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846561		cis	Lymphoblastoid	GTEx
rs16846561	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173855600-173875400	Weak transcription	NH-A	brain
2	chr1:173855800-173873000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
4	chr1:173856000-173869400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:173856000-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:173856000-173872600	Weak transcription	Fetal Thymus	thymus
7	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
8	chr1:173856200-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:173856200-173872800	Weak transcription	Ovary	ovary
10	chr1:173856200-173875400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173856200-173878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
13	chr1:173856400-173873800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:173856400-173876000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:173856400-173880000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:173856600-173881200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
18	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:173857400-173869400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:173857400-173880400	Weak transcription	Fetal Brain Female	brain
21	chr1:173857400-173881800	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:173857400-173884400	Weak transcription	HepG2	liver
23	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
25	chr1:173857600-173870000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:173857600-173872600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
28	chr1:173858400-173878600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:173858600-173881400	Weak transcription	Primary B cells from cord blood	blood
30	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
31	chr1:173858800-173871400	Weak transcription	HSMM	muscle
32	chr1:173858800-173872200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:173858800-173876000	Weak transcription	NHLF	lung
34	chr1:173860200-173869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:173862000-173873400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:173862200-173872000	Weak transcription	Fetal Lung	lung
38	chr1:173863600-173875800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:173863800-173878800	Weak transcription	Aorta	Aorta
40	chr1:173864000-173875600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:173864200-173878600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:173864600-173869600	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:173864600-173871800	Weak transcription	Fetal Stomach	stomach
44	chr1:173864600-173878200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:173865200-173874600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:173865400-173869400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:173865400-173873200	Weak transcription	Primary T cells from cord blood	blood
49	chr1:173866600-173878600	Strong transcription	Liver	Liver
50	chr1:173867000-173869600	Weak transcription	H1 Cell Line	embryonic stem cell

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