Variant report

Variant	rs2192015
Chromosome Location	chr2:72501137-72501138
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	chr2:72496641..72498799-chr2:72499745..72502652,2	K562	blood:

Extended variants
information (count: 139 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10168145	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10173381	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs10175915	0.80[GIH][hapmap]
rs10186080	1.00[CHB][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203965	1.00[CHB][hapmap]
rs10204415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs10205108	0.84[GIH][hapmap]
rs10207299	1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10209861	0.85[AMR][1000 genomes]
rs10221769	0.84[GIH][hapmap]
rs11126366	1.00[CHB][hapmap]
rs1159764	0.84[GIH][hapmap]
rs1159766	0.84[GIH][hapmap]
rs11690734	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11694921	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11902025	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12466613	1.00[CHB][hapmap]
rs12467816	1.00[CHB][hapmap]
rs12468057	1.00[CHB][hapmap]
rs12471875	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs13383535	1.00[CHB][hapmap]
rs13390754	1.00[CHB][hapmap]
rs13395204	0.92[AFR][1000 genomes]
rs13409513	1.00[CHB][hapmap]
rs13409641	1.00[CHB][hapmap]
rs13417114	0.88[GIH][hapmap]
rs13423761	0.88[AFR][1000 genomes]
rs13432350	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap]
rs1568145	1.00[CHB][hapmap]
rs17724860	0.80[GIH][hapmap]
rs17725024	0.80[GIH][hapmap]
rs194235	0.92[GIH][hapmap]
rs2041563	0.92[GIH][hapmap]
rs2041564	0.83[AFR][1000 genomes]
rs2109960	1.00[CHB][hapmap]
rs2109961	0.83[ASN][1000 genomes]
rs2109963	0.92[GIH][hapmap];0.85[MKK][hapmap];0.80[AMR][1000 genomes]
rs2192014	1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2203679	1.00[CHB][hapmap]
rs2420442	0.83[ASN][1000 genomes]
rs2420444	1.00[CHB][hapmap]
rs2901144	0.83[ASN][1000 genomes]
rs2901146	1.00[CHB][hapmap]
rs3115351	1.00[CHB][hapmap]
rs41386	0.80[GIH][hapmap]
rs41388	0.84[GIH][hapmap]
rs41389	0.84[GIH][hapmap]
rs41393	0.84[GIH][hapmap]
rs41394	0.84[GIH][hapmap]
rs41401	0.92[GIH][hapmap]
rs41402	0.92[GIH][hapmap]
rs41403	0.84[GIH][hapmap]
rs41407	0.84[GIH][hapmap]
rs41413	0.84[GIH][hapmap]
rs41417	0.80[GIH][hapmap]
rs4852285	0.88[AFR][1000 genomes]
rs4852286	1.00[CHB][hapmap]
rs4852287	1.00[CHB][hapmap]
rs4852288	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs585653	1.00[CHB][hapmap]
rs587431	1.00[CHB][hapmap]
rs587744	1.00[CHB][hapmap]
rs589547	1.00[CHB][hapmap]
rs590252	1.00[CHB][hapmap]
rs590345	1.00[CHB][hapmap]
rs598138	1.00[CHB][hapmap]
rs598496	1.00[CHB][hapmap]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap]
rs614653	1.00[CHB][hapmap]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CHB][hapmap]
rs630241	1.00[CHB][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634785	1.00[CHB][hapmap]
rs634929	1.00[CHB][hapmap]
rs636319	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap]
rs638854	1.00[CHB][hapmap]
rs640610	1.00[CHB][hapmap]
rs641123	1.00[CHB][hapmap]
rs641939	1.00[CHB][hapmap]
rs642652	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs647242	1.00[CHB][hapmap]
rs647269	1.00[CHB][hapmap]
rs6546753	0.92[GIH][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6546755	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6546756	1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6546760	1.00[CHB][hapmap]
rs6546764	1.00[CHB][hapmap]
rs6546765	1.00[CHB][hapmap]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CHB][hapmap]
rs663218	1.00[CHB][hapmap]
rs666233	1.00[CHB][hapmap]
rs666361	1.00[CHB][hapmap]
rs669074	1.00[CHB][hapmap]
rs6709109	0.83[ASN][1000 genomes]
rs6722637	0.83[ASN][1000 genomes]
rs6729863	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6733210	1.00[CHB][hapmap]
rs6742264	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6748607	0.83[AFR][1000 genomes]
rs674863	1.00[CHB][hapmap]
rs6751276	0.83[AFR][1000 genomes]
rs6752122	1.00[CHB][hapmap]
rs6753073	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6758462	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6760895	0.92[GIH][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CHB][hapmap]
rs681574	1.00[CHB][hapmap]
rs687325	1.00[CHB][hapmap]
rs687371	1.00[CHB][hapmap]
rs688433	1.00[CHB][hapmap]
rs689154	1.00[CHB][hapmap]
rs719118	0.83[ASN][1000 genomes]
rs7558686	1.00[CHB][hapmap]
rs7558919	1.00[CHB][hapmap]
rs7559131	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs7565922	0.92[GIH][hapmap]
rs7568803	1.00[CHB][hapmap]
rs7577877	1.00[CHB][hapmap]
rs7583271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs7594350	1.00[CHB][hapmap]
rs7595180	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs768042	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs768043	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9309464	1.00[CHB][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	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2192015	TGFA	cis	cerebellum	SCAN
rs2192015	MPHOSPH10	cis	cerebellum	SCAN
rs2192015	CCT7	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72485200-72501800	Weak transcription	HSMMtube	muscle
2	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
3	chr2:72491200-72502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:72497200-72503400	Enhancers	Fetal Intestine Large	intestine
5	chr2:72497400-72505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:72498000-72503000	Enhancers	Fetal Intestine Small	intestine
7	chr2:72498200-72501600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr2:72498200-72502400	Flanking Active TSS	A549	lung
9	chr2:72498400-72502800	Enhancers	Duodenum Mucosa	Duodenum
10	chr2:72499000-72502400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:72499400-72502200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:72499400-72503000	Weak transcription	Left Ventricle	heart
13	chr2:72499400-72507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:72499400-72507800	Weak transcription	Psoas Muscle	Psoas
15	chr2:72499600-72501400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:72499600-72501600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:72499600-72501800	Weak transcription	Brain Germinal Matrix	brain
18	chr2:72499600-72501800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:72499600-72502200	Weak transcription	Small Intestine	intestine
20	chr2:72499600-72502800	Weak transcription	Right Atrium	heart
21	chr2:72499600-72510400	Weak transcription	Right Ventricle	heart
22	chr2:72499800-72501400	Weak transcription	Liver	Liver
23	chr2:72499800-72501400	Weak transcription	Fetal Lung	lung
24	chr2:72499800-72501600	Weak transcription	Brain Anterior Caudate	brain
25	chr2:72499800-72501600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:72499800-72501800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:72499800-72502000	Weak transcription	Fetal Brain Male	brain
28	chr2:72499800-72502400	Weak transcription	Ovary	ovary
29	chr2:72499800-72505200	Weak transcription	NHEK	skin
30	chr2:72500000-72501600	Weak transcription	Fetal Heart	heart
31	chr2:72500200-72502000	Weak transcription	Fetal Kidney	kidney
32	chr2:72500400-72501800	Enhancers	Stomach Mucosa	stomach
33	chr2:72500400-72502200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:72500600-72502800	Enhancers	Hela-S3	cervix
35	chr2:72500600-72503600	Enhancers	Brain Substantia Nigra	brain
36	chr2:72501000-72502600	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr2:72501000-72503000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:72501000-72505800	Weak transcription	Pancreas	Pancrea

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