Variant report

Variant	rs4324292
Chromosome Location	chr2:172813245-172813246
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172807381..172810249-chr2:172812203..172814108,2	K562	blood:
2	chr2:172811747..172815562-chr2:172948596..172951136,4	MCF-7	breast:
3	chr2:172807954..172811723-chr2:172812087..172815837,4	K562	blood:
4	chr2:172813132..172813902-chr2:172968337..172969167,2	K562	blood:
5	chr2:172778822..172781604-chr2:172813055..172814989,2	MCF-7	breast:
6	chr2:172813074..172816738-chr2:172958355..172960907,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction
ENSG00000128708	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10166352	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10177679	0.88[JPT][hapmap]
rs10188587	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10196521	0.88[JPT][hapmap]
rs1022358	0.88[JPT][hapmap]
rs10439296	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10930496	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10930498	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10930500	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10930501	0.81[AFR][1000 genomes]
rs11676484	0.88[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs11677573	0.88[JPT][hapmap]
rs11692418	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11695887	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11883977	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12467010	0.89[AFR][1000 genomes]
rs12468218	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12478215	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12617265	0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12619137	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12692977	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12692979	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13017988	0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13018515	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13021571	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13399316	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1400816	0.89[JPT][hapmap]
rs1443700	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1607253	0.89[JPT][hapmap]
rs1878583	0.88[JPT][hapmap]
rs1982288	0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2028670	0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2028671	0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2028672	0.89[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes]
rs2028673	0.83[AFR][1000 genomes]
rs2028674	0.83[AFR][1000 genomes]
rs2056202	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2138873	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2176466	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2292813	0.88[JPT][hapmap]
rs2357064	0.89[JPT][hapmap]
rs2357206	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2357207	0.89[AFR][1000 genomes]
rs2357208	0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs28372952	0.88[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2884123	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3770443	0.89[JPT][hapmap]
rs3770453	0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs3770457	0.89[JPT][hapmap]
rs3821092	0.86[JPT][hapmap]
rs3821094	0.88[JPT][hapmap]
rs3821096	0.88[JPT][hapmap]
rs4072279	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4668413	0.88[EUR][1000 genomes]
rs4668415	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4668416	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4668417	0.88[JPT][hapmap]
rs4668419	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59853867	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60315614	0.83[AMR][1000 genomes]
rs60706248	0.89[AFR][1000 genomes]
rs62182438	0.85[ASN][1000 genomes]
rs6433313	0.88[JPT][hapmap]
rs6433315	0.88[JPT][hapmap]
rs6433317	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433318	0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6433322	0.82[YRI][hapmap]
rs6707142	0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6708365	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6709299	0.81[EUR][1000 genomes]
rs6711813	0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6714214	0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6726050	0.98[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6726991	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6727459	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6736159	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6740705	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6741030	0.93[AFR][1000 genomes]
rs6753551	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6753859	0.88[JPT][hapmap]
rs6757680	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6758494	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6760680	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7340516	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7371503	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7579509	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7580132	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7580232	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7588025	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7594478	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs925881	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs949548	0.88[JPT][hapmap]
rs9636293	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs970948	0.88[JPT][hapmap]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4324292	AC068039.4	cis	Stomach	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172779800-172828400	Weak transcription	Aorta	Aorta
2	chr2:172780000-172829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:172780200-172822200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:172780200-172840400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:172780400-172820600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:172780600-172820600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:172780600-172822200	Weak transcription	Liver	Liver
9	chr2:172780600-172822200	Weak transcription	Fetal Kidney	kidney
10	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
12	chr2:172781400-172822000	Weak transcription	HUVEC	blood vessel
13	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:172784600-172815000	Weak transcription	Left Ventricle	heart
15	chr2:172785400-172822200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:172785400-172822400	Weak transcription	Placenta	Placenta
17	chr2:172785800-172822200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:172787800-172822200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:172790400-172825200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:172793000-172817200	Weak transcription	Right Atrium	heart
21	chr2:172796000-172855200	Weak transcription	Gastric	stomach
22	chr2:172796800-172820600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:172796800-172832200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:172797000-172822200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:172797000-172822200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:172798200-172822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:172798200-172822600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:172798400-172820600	Weak transcription	Brain Germinal Matrix	brain
29	chr2:172805000-172822200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:172805400-172822000	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:172806400-172822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:172807400-172845400	Weak transcription	Spleen	Spleen
33	chr2:172807600-172822400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:172808000-172847200	Weak transcription	Fetal Brain Female	brain
35	chr2:172808000-172849400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:172808200-172814200	Strong transcription	Dnd41	blood
37	chr2:172808800-172814000	Strong transcription	Fetal Thymus	thymus
38	chr2:172809000-172822600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:172809400-172813600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:172809400-172814000	Strong transcription	Fetal Muscle Leg	muscle
41	chr2:172809600-172813600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:172809600-172817400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr2:172809800-172837800	Weak transcription	Esophagus	oesophagus
44	chr2:172810000-172819200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:172810200-172822200	Weak transcription	Thymus	Thymus
47	chr2:172810400-172825400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:172810800-172814400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:172811200-172814000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr2:172811200-172814000	Strong transcription	Fetal Lung	lung

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