Variant report

Variant	rs17036129
Chromosome Location	chr4:106624529-106624530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106619010..106621015-chr4:106623731..106625393,2	K562	blood:
2	chr4:106622664..106627326-chr4:106627806..106630924,8	MCF-7	breast:
3	chr4:106619847..106624541-chr4:106627186..106631133,7	MCF-7	breast:
4	chr4:106623594..106626917-chr4:106627781..106630373,5	K562	blood:
5	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:

Variant related genes	Relation type
ENSG00000138785	Chromatin interaction
ENSG00000236699	Chromatin interaction
ENSG00000138780	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10050159	1.00[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs10050333	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10516525	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10516526	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10516527	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10516528	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10516529	0.87[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11097901	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11722225	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11723225	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11723240	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11723639	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11724839	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11724884	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11725523	1.00[CEU][hapmap]
rs11726094	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726124	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726569	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11726674	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11727189	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727348	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11727500	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11727735	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727745	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11728044	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11728716	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11728918	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11729003	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11730354	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11730365	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11730660	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11731386	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11731417	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11731714	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11731938	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11732298	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11732629	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11732650	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11733093	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11733124	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11733150	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11733223	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11733225	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11733287	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11733654	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11734568	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11734571	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11735213	1.00[CEU][hapmap]
rs11735527	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11735851	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11736834	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11736859	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11737335	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11737741	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12374256	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1374531	1.00[CEU][hapmap]
rs17035917	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs17035960	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs17035971	0.84[AMR][1000 genomes]
rs17036027	0.84[AMR][1000 genomes]
rs17036052	0.84[AMR][1000 genomes]
rs17036066	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17036090	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17036105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036120	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036123	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036125	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036139	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036142	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036156	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036177	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036189	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036225	1.00[CEU][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036230	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036258	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17036292	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17036308	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17036310	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17036327	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17036337	1.00[MEX][hapmap]
rs17036341	0.81[EUR][1000 genomes]
rs17331332	0.87[CEU][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28488297	0.83[EUR][1000 genomes]
rs34072732	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35370743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35808787	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4373160	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58775257	0.81[EUR][1000 genomes]
rs67277942	0.81[EUR][1000 genomes]
rs72669974	0.84[AMR][1000 genomes]
rs72669978	0.84[AMR][1000 genomes]
rs72669980	0.84[AMR][1000 genomes]
rs72669981	0.84[AMR][1000 genomes]
rs72669992	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72669993	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72669995	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72669997	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72669998	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72670002	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72671805	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671808	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671809	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671811	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671815	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671824	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671828	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671835	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671836	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671837	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671840	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671844	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671849	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671852	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671853	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72671854	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671855	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671856	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671858	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671861	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671862	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671863	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671866	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671869	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671870	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671871	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671873	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671874	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671878	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671879	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671880	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671881	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671885	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671886	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671889	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671892	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671895	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72671896	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673803	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673805	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673811	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673812	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673813	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673817	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72673821	0.85[AMR][1000 genomes]
rs72673822	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673823	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673824	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673828	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673831	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673832	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673834	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72673853	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673855	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673858	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673860	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673865	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673870	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673872	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673873	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72673888	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72673889	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72673891	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7676975	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17036129	INTS12	cis	brain	seeQTL
rs17036129	INTS12	cis	lymphoblastoid	seeQTL
rs17036129	INTS12	trans	brain	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106587800-106629000	Weak transcription	Lung	lung
2	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
3	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
4	chr4:106601200-106628400	Weak transcription	Psoas Muscle	Psoas
5	chr4:106602200-106629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106602400-106628600	Weak transcription	Right Ventricle	heart
7	chr4:106602600-106628400	Weak transcription	Fetal Heart	heart
8	chr4:106602600-106629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:106604400-106629200	Weak transcription	Esophagus	oesophagus
10	chr4:106604400-106629200	Weak transcription	Gastric	stomach
11	chr4:106606600-106628200	Weak transcription	Hela-S3	cervix
12	chr4:106607600-106626400	Weak transcription	Small Intestine	intestine
13	chr4:106609200-106625200	Strong transcription	HSMM	muscle
14	chr4:106610400-106628800	Weak transcription	Fetal Kidney	kidney
15	chr4:106610600-106628200	Weak transcription	Fetal Brain Male	brain
16	chr4:106610600-106628600	Weak transcription	A549	lung
17	chr4:106610800-106628600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:106611400-106627600	Weak transcription	HepG2	liver
19	chr4:106611400-106628600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:106612400-106624600	Weak transcription	NHEK	skin
21	chr4:106613600-106628600	Weak transcription	Aorta	Aorta
22	chr4:106613600-106628600	Weak transcription	Ovary	ovary
23	chr4:106614600-106628400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:106614800-106628200	Weak transcription	Brain Angular Gyrus	brain
25	chr4:106615000-106628600	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:106615400-106625000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:106615400-106626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:106615800-106628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:106615800-106628600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:106616000-106628400	Weak transcription	NHLF	lung
31	chr4:106616000-106628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:106616000-106629000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:106616200-106624600	Weak transcription	HSMMtube	muscle
34	chr4:106616200-106628400	Weak transcription	Brain Germinal Matrix	brain
35	chr4:106616400-106628400	Weak transcription	Thymus	Thymus
36	chr4:106616400-106628600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:106616800-106628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:106616800-106628600	Weak transcription	NH-A	brain
39	chr4:106617400-106627600	Weak transcription	Fetal Intestine Small	intestine
40	chr4:106617400-106628600	Weak transcription	Fetal Intestine Large	intestine
41	chr4:106617400-106628800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:106617400-106629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:106617400-106629000	Weak transcription	Pancreas	Pancrea
44	chr4:106617600-106626200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:106617600-106628000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:106617600-106628400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:106617600-106628400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:106618200-106626400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:106619200-106624600	Weak transcription	Liver	Liver
50	chr4:106619200-106628600	Weak transcription	Fetal Stomach	stomach

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