Variant report

Variant	rs4597559
Chromosome Location	chr2:191321797-191321798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10931455	0.90[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10931459	0.90[CEU][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10931460	0.90[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10931464	0.86[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11673788	0.82[ASW][hapmap];0.90[CEU][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11673921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674229	0.82[EUR][1000 genomes]
rs11675051	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11677333	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685221	0.90[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11686226	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11695681	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11891641	0.88[JPT][hapmap]
rs13005335	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17801596	0.82[EUR][1000 genomes]
rs2159822	0.86[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34101385	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34109383	0.85[EUR][1000 genomes]
rs34703964	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34751744	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35954637	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36064835	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934784	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4324341	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4343493	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384819	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4384820	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4638823	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853701	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55784091	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55788736	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55884870	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55901912	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55918914	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56094872	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56337518	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61730953	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61743479	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62180963	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62180964	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62180981	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62180988	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62180989	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62181001	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181002	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181014	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181015	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181024	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62181026	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62181027	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62181031	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62181032	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62181033	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62181036	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62181053	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62181057	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62182860	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62182861	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62182862	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62182863	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62182864	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62182892	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62182893	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6707836	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6708018	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6714829	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6719656	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6725814	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6727054	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6742904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753226	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757698	0.90[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72903331	0.82[EUR][1000 genomes]
rs72905231	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905290	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907168	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72911128	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7572139	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7573621	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7574871	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7721	0.82[ASW][hapmap];0.90[CEU][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[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	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv962094	chr2:191318806-191324621	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4597559	TMEM194B	cis	Thyroid	GTEx
rs4597559	TMEM194B	cis	Adipose Subcutaneous	GTEx
rs4597559	MFSD6	cis	lymphoblastoid	seeQTL
rs4597559	INPP1	cis	cerebellum	SCAN
rs4597559	ZC3H15	cis	cerebellum	SCAN
rs4597559	HIBCH	cis	lymphoblastoid	seeQTL
rs4597559	FLJ20160	cis	multi-tissue	Pritchard
rs4597559	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs4597559	HIBCH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191302400-191331000	Weak transcription	A549	lung
2	chr2:191303800-191331600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:191303800-191332600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
5	chr2:191307600-191322600	Weak transcription	Aorta	Aorta
6	chr2:191308000-191328800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:191308800-191327200	Weak transcription	Right Atrium	heart
8	chr2:191309200-191322400	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:191309400-191331400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:191310200-191323600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:191310400-191331600	Weak transcription	Stomach Mucosa	stomach
12	chr2:191311400-191324200	Weak transcription	Fetal Heart	heart
13	chr2:191311600-191331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:191311800-191324600	Weak transcription	Left Ventricle	heart
15	chr2:191311800-191331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:191311800-191331400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:191311800-191331600	Weak transcription	Ovary	ovary
18	chr2:191312000-191332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:191312200-191324400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:191313000-191331400	Weak transcription	HSMMtube	muscle
21	chr2:191313000-191333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:191313800-191323600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:191314000-191331600	Weak transcription	Fetal Kidney	kidney
24	chr2:191315800-191327400	Weak transcription	Spleen	Spleen
25	chr2:191316600-191321800	Weak transcription	Primary B cells from cord blood	blood
26	chr2:191316600-191323400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:191316600-191324600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:191316600-191325200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:191316600-191331200	Weak transcription	NHLF	lung
30	chr2:191317000-191323600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:191317600-191321800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr2:191317600-191331600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:191318000-191322800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:191318600-191325200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:191318800-191324600	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:191318800-191324600	Weak transcription	Brain Substantia Nigra	brain
37	chr2:191319400-191322000	Strong transcription	Fetal Brain Female	brain
38	chr2:191319400-191323600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:191319400-191331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:191319400-191332000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:191319600-191323400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:191320200-191323000	Strong transcription	Fetal Thymus	thymus
43	chr2:191320800-191322600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:191320800-191327800	Strong transcription	Primary T cells from cord blood	blood
45	chr2:191321000-191322000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:191321000-191322800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr2:191321000-191323000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:191321000-191323000	Strong transcription	Thymus	Thymus
49	chr2:191321000-191323200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:191321000-191323400	Strong transcription	Primary monocytes fromperipheralblood	blood

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