Variant report

Variant	rs6542837
Chromosome Location	chr2:99444701-99444702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99434724..99436246-chr2:99444476..99446332,2	MCF-7	breast:
2	chr2:99437609..99439814-chr2:99443387..99445956,2	MCF-7	breast:
3	chr2:99443633..99446031-chr2:99448768..99450507,2	K562	blood:
4	chr2:99344971..99347100-chr2:99444571..99447459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction
ENSG00000071073	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10174531	0.86[ASN][1000 genomes]
rs10175560	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10182043	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123754	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11900176	0.83[ASW][hapmap];0.82[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11900524	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12478574	0.80[EUR][1000 genomes]
rs12712034	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12712037	0.82[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12990579	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13005148	0.82[EUR][1000 genomes]
rs2276604	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs2280142	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35077008	0.80[EUR][1000 genomes]
rs35109359	0.80[EUR][1000 genomes]
rs35929117	0.81[EUR][1000 genomes]
rs4499468	0.80[EUR][1000 genomes]
rs6542839	0.81[MEX][hapmap]
rs6714330	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739097	0.83[EUR][1000 genomes]
rs6753465	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753879	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6755640	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757098	0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs6760065	0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs73962464	0.85[ASN][1000 genomes]
rs7423519	0.85[MEX][hapmap]
rs7560696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7565614	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7565736	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7590596	0.82[EUR][1000 genomes]
rs885115	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6542837	TSGA10	cis	cerebellum	SCAN
rs6542837	TSGA10	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99438800-99448600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:99439800-99446200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:99439800-99448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:99440000-99447600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:99440200-99449800	Weak transcription	Colonic Mucosa	Colon
7	chr2:99440400-99453800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:99440600-99445600	Weak transcription	Right Atrium	heart
10	chr2:99440600-99445600	Weak transcription	Spleen	Spleen
11	chr2:99440600-99449600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:99440600-99449600	Weak transcription	HMEC	breast
13	chr2:99440600-99453800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:99441000-99445200	Weak transcription	Thymus	Thymus
15	chr2:99441000-99449600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:99441400-99445200	Weak transcription	HUVEC	blood vessel
17	chr2:99441800-99445600	Weak transcription	Lung	lung
18	chr2:99441800-99446600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:99441800-99449000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:99442200-99445200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:99442400-99445600	Weak transcription	Left Ventricle	heart
22	chr2:99442600-99449800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:99442800-99444800	Weak transcription	Primary B cells from cord blood	blood
24	chr2:99442800-99444800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:99442800-99445000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:99443000-99445600	Weak transcription	Stomach Mucosa	stomach
27	chr2:99443000-99448600	Weak transcription	Brain Angular Gyrus	brain
28	chr2:99443000-99448600	Weak transcription	Right Ventricle	heart
29	chr2:99443200-99444800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:99443600-99450400	Weak transcription	Pancreas	Pancrea
31	chr2:99443800-99447800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:99443800-99448600	Weak transcription	Esophagus	oesophagus
33	chr2:99443800-99449600	Weak transcription	Gastric	stomach
34	chr2:99444000-99444800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:99444000-99445600	Enhancers	Dnd41	blood
36	chr2:99444000-99446600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:99444000-99447400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:99444200-99444800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:99444200-99445400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:99444200-99446400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:99444200-99446400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr2:99444200-99446800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr2:99444200-99446800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:99444200-99447000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr2:99444200-99447600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr2:99444200-99448000	Enhancers	Fetal Thymus	thymus
47	chr2:99444200-99450800	Enhancers	HepG2	liver
48	chr2:99444200-99451000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:99444400-99445000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:99444400-99446600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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