Variant report

Variant	rs17036105
Chromosome Location	chr4:106603272-106603273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:106603105-106603305	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:106602245..106604100-chr4:106629156..106631136,2	MCF-7	breast:
2	chr4:106602488..106605475-chr4:106815984..106818192,2	MCF-7	breast:
3	chr4:105887751..105889540-chr4:106602331..106605002,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248778	TF binding region
ENSG00000168743	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000138780	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10050159	0.83[EUR][1000 genomes]
rs10050333	0.83[EUR][1000 genomes]
rs10516525	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10516526	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10516527	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10516528	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10516529	0.81[EUR][1000 genomes]
rs11097901	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11722225	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11723225	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	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11724884	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11726094	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726124	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726569	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11726674	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11727189	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727348	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11727500	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11727735	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727745	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11728044	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11728716	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	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	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11732629	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11732650	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	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11733225	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11733287	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]
rs11735527	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11735851	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11736834	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11736859	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	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17035960	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]
rs17036120	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036123	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036125	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036139	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036142	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036156	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	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17036230	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]
rs17036341	0.81[EUR][1000 genomes]
rs17331332	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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17036105	INTS12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106578600-106607000	Weak transcription	Small Intestine	intestine
2	chr4:106580400-106603400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:106580400-106613200	Weak transcription	Fetal Intestine Small	intestine
4	chr4:106587800-106629000	Weak transcription	Lung	lung
5	chr4:106593000-106603800	Weak transcription	Aorta	Aorta
6	chr4:106594000-106603400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:106597000-106610000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:106597200-106603400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:106598600-106613000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:106599000-106603600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:106599000-106614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:106599200-106613800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:106599800-106603600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
15	chr4:106600600-106603400	Weak transcription	NHDF-Ad	bronchial
16	chr4:106600600-106603600	Weak transcription	NH-A	brain
17	chr4:106600600-106603800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:106600600-106603800	Weak transcription	Ovary	ovary
19	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
20	chr4:106600800-106603400	Weak transcription	HSMMtube	muscle
21	chr4:106600800-106603600	Weak transcription	HUVEC	blood vessel
22	chr4:106600800-106603800	Weak transcription	Fetal Kidney	kidney
23	chr4:106600800-106603800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:106601000-106603800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:106601000-106603800	Weak transcription	Osteobl	bone
26	chr4:106601200-106603800	Weak transcription	Primary T cells from cord blood	blood
27	chr4:106601200-106603800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:106601200-106603800	Weak transcription	Pancreas	Pancrea
29	chr4:106601200-106603800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:106601200-106603800	Weak transcription	HSMM	muscle
31	chr4:106601200-106604000	Weak transcription	Gastric	stomach
32	chr4:106601200-106604000	Weak transcription	HepG2	liver
33	chr4:106601200-106607000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:106601200-106609600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:106601200-106628400	Weak transcription	Psoas Muscle	Psoas
36	chr4:106601400-106603400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:106601400-106603800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:106601600-106603400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:106601600-106604000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:106601600-106607000	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:106601600-106609200	Weak transcription	A549	lung
42	chr4:106601800-106603400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:106601800-106603400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:106601800-106603400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:106601800-106603400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:106601800-106603400	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:106601800-106603800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:106601800-106612600	Weak transcription	Fetal Brain Female	brain
49	chr4:106602000-106604000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:106602000-106604000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links