Variant report

Variant	rs2593181
Chromosome Location	chr15:52196153-52196154
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52194606..52197344-chr15:52198863..52200603,2	MCF-7	breast:
2	chr15:52184376..52187037-chr15:52195725..52198410,2	K562	blood:
3	chr15:52194540..52196251-chr15:52201951..52203971,2	K562	blood:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000272337	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1025184	0.85[CEU][hapmap]
rs1035737	0.85[CEU][hapmap]
rs11049	0.84[CEU][hapmap]
rs11070865	0.85[CEU][hapmap]
rs11070868	0.85[CEU][hapmap]
rs1133883	0.83[CEU][hapmap]
rs11630579	0.84[CEU][hapmap]
rs11630943	0.85[CEU][hapmap]
rs11637876	0.85[CEU][hapmap]
rs12593708	0.86[CEU][hapmap]
rs12905283	0.85[CEU][hapmap]
rs12908327	0.85[CEU][hapmap]
rs12915015	0.88[CEU][hapmap]
rs12915568	0.83[CEU][hapmap]
rs16953082	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964482	1.00[CHB][hapmap]
rs16964483	1.00[CHB][hapmap]
rs16964486	1.00[JPT][hapmap]
rs16964505	1.00[JPT][hapmap]
rs16964506	0.82[JPT][hapmap]
rs16964508	0.82[JPT][hapmap]
rs16964532	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964555	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964561	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964579	0.90[ASN][1000 genomes]
rs16964585	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964596	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16964639	0.90[ASN][1000 genomes]
rs16964645	0.90[ASN][1000 genomes]
rs17526463	0.85[CEU][hapmap]
rs17526760	0.85[CEU][hapmap]
rs17611193	0.85[CEU][hapmap]
rs17611465	1.00[CHB][hapmap]
rs1840708	0.85[CEU][hapmap]
rs1863429	0.84[AMR][1000 genomes]
rs1863430	0.83[CEU][hapmap]
rs1972419	0.89[AMR][1000 genomes]
rs1991267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007335	0.83[CEU][hapmap]
rs2007355	0.82[CEU][hapmap]
rs2009972	0.89[CEU][hapmap]
rs2010026	0.83[CEU][hapmap]
rs2011995	0.83[CEU][hapmap]
rs2016057	1.00[CHB][hapmap]
rs2034856	0.85[CEU][hapmap]
rs2052705	0.82[CEU][hapmap]
rs2052706	0.84[CEU][hapmap]
rs2052708	0.83[CEU][hapmap]
rs2052709	0.83[CEU][hapmap]
rs2114191	0.85[CEU][hapmap]
rs2241503	0.82[CEU][hapmap]
rs2252606	0.82[CEU][hapmap]
rs2252831	0.88[CEU][hapmap]
rs2253116	0.85[CEU][hapmap]
rs2258248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414115	1.00[JPT][hapmap]
rs2433217	0.85[CEU][hapmap]
rs2433221	0.82[CEU][hapmap]
rs2436655	0.83[CEU][hapmap]
rs2436656	0.83[CEU][hapmap]
rs2436660	0.85[CEU][hapmap]
rs2441780	0.85[CEU][hapmap]
rs2448945	1.00[CHB][hapmap]
rs2448946	0.83[CEU][hapmap]
rs2448950	0.83[CEU][hapmap]
rs2448953	0.82[CEU][hapmap]
rs2470612	0.85[CEU][hapmap]
rs2554314	0.83[CEU][hapmap]
rs2554327	0.85[CEU][hapmap]
rs2554348	0.93[CEU][hapmap]
rs2554349	0.85[CEU][hapmap]
rs2554354	1.00[CHB][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes]
rs2570230	1.00[CHB][hapmap]
rs2570239	0.85[CEU][hapmap]
rs2570241	0.85[CEU][hapmap]
rs2570243	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs2570265	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593170	0.85[CEU][hapmap]
rs2593173	0.85[CEU][hapmap]
rs2593184	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593187	0.83[CEU][hapmap]
rs2593188	0.85[CEU][hapmap]
rs2593199	0.82[CEU][hapmap]
rs2593202	0.83[CEU][hapmap]
rs2622765	1.00[CHB][hapmap]
rs2622778	1.00[CHB][hapmap]
rs2623245	1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes]
rs2623247	1.00[CHB][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2623251	1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes]
rs2623255	0.85[CEU][hapmap]
rs2623258	1.00[CHB][hapmap]
rs2623263	1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2623271	0.85[CEU][hapmap]
rs2623280	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2623281	0.83[CEU][hapmap]
rs2623282	0.83[CEU][hapmap]
rs2623283	0.86[CEU][hapmap]
rs2623291	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	1.00[CHB][hapmap]
rs2899478	1.00[JPT][hapmap]
rs2912186	0.83[CEU][hapmap]
rs2912187	0.85[CEU][hapmap]
rs2912189	0.85[CEU][hapmap]
rs2916169	0.83[CEU][hapmap]
rs2916172	0.85[CEU][hapmap]
rs2916176	0.85[CEU][hapmap]
rs2916177	0.85[CEU][hapmap]
rs2929423	0.83[CEU][hapmap]
rs2929424	0.83[CEU][hapmap]
rs2929425	0.85[CEU][hapmap]
rs2929426	0.85[CEU][hapmap]
rs2959285	0.89[CEU][hapmap]
rs2959293	0.82[CEU][hapmap]
rs2959296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959298	0.85[CEU][hapmap]
rs2959299	0.85[CEU][hapmap]
rs3751595	1.00[JPT][hapmap]
rs3794532	0.83[CEU][hapmap]
rs6493520	0.85[CEU][hapmap]
rs6493521	0.83[CEU][hapmap]
rs6493525	0.85[CEU][hapmap]
rs6493526	0.85[CEU][hapmap]
rs7162925	0.88[CEU][hapmap]
rs7163541	0.83[CEU][hapmap]
rs7165594	1.00[JPT][hapmap]
rs7167759	1.00[JPT][hapmap]
rs7168659	0.83[CEU][hapmap]
rs7170091	0.83[CEU][hapmap]
rs7171796	0.83[CEU][hapmap]
rs7174497	0.85[CEU][hapmap]
rs7174808	0.85[CEU][hapmap]
rs7178561	0.83[CEU][hapmap]
rs7178776	0.83[CEU][hapmap]
rs7179599	0.83[CEU][hapmap]
rs7181540	0.83[CEU][hapmap]
rs726158	0.83[CEU][hapmap]
rs8028922	0.85[CEU][hapmap]
rs8038344	0.83[CEU][hapmap]
rs9944235	0.83[CEU][hapmap]

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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2593181	SCG3	cis	Brain Pons	GTEx
rs2593181	SCG3	cis	Frontal Cortex	GTEx
rs2593181	RP11-707P17.1	cis	Nerve Tibial	GTEx
rs2593181	SCG3	cis	Cerebellum	GTEx
rs2593181	SCG3	cis	Temporal Cortex	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
2	chr15:52167200-52210800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:52167600-52199600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52171000-52210800	Weak transcription	Right Ventricle	heart
5	chr15:52172800-52208200	Weak transcription	Brain Angular Gyrus	brain
6	chr15:52177200-52213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:52178800-52216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:52179000-52196400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:52179000-52196600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:52179000-52196600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:52179600-52203800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:52179800-52197200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:52179800-52197400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:52179800-52201600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:52179800-52218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:52180000-52197400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr15:52180200-52199400	Strong transcription	NHEK	skin
19	chr15:52180400-52218200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:52181400-52197000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr15:52181600-52196200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:52181600-52196200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:52181600-52197400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:52181600-52197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:52181600-52203400	Strong transcription	Dnd41	blood
27	chr15:52181800-52203400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:52182800-52198600	Strong transcription	HMEC	breast
29	chr15:52183000-52203400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:52183400-52203200	Strong transcription	Primary T cells from cord blood	blood
32	chr15:52183600-52197400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:52183600-52197600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr15:52183600-52199000	Strong transcription	Fetal Intestine Large	intestine
35	chr15:52183800-52197600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:52183800-52198200	Strong transcription	Liver	Liver
37	chr15:52184400-52205000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52185000-52196800	Weak transcription	Stomach Mucosa	stomach
39	chr15:52185600-52200000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr15:52185800-52197000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:52185800-52197600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52185800-52204200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr15:52186000-52197000	Strong transcription	NH-A	brain
44	chr15:52186000-52197200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:52186200-52196200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:52186200-52197200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:52186200-52204200	Strong transcription	Primary B cells from cord blood	blood
48	chr15:52186400-52197200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:52186400-52197200	Strong transcription	GM12878-XiMat	blood
50	chr15:52186400-52199400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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