Variant report

Variant	rs2097461
Chromosome Location	chr22:29191879-29191880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29189733-29194459	GM18526	blood:	n/a	n/a
2	POLR2A	chr22:29189763-29192238	GM12892	blood:	n/a	n/a
3	POLR2A	chr22:29191651-29192341	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:29188029-29193150	GM12892	blood:	n/a	n/a
5	POLR2A	chr22:29191721-29192018	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr22:29188530-29193620	GM19193	blood:	n/a	n/a
7	POLR2A	chr22:29188700-29193625	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr22:29189651-29193756	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:29191723-29192219	HepG2	liver:	n/a	n/a
10	POLR2A	chr22:29189960-29191964	A549	lung:	n/a	n/a
11	POLR2A	chr22:29188106-29198866	HepG2	liver:	n/a	n/a
12	POLR2A	chr22:29191774-29191953	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr22:29188141-29193821	HepG2	liver:	n/a	n/a
14	POLR2A	chr22:29188193-29193681	GM19099	blood:	n/a	n/a
15	POLR2A	chr22:29189781-29193210	GM15510	blood:	n/a	n/a
16	POLR2A	chr22:29188206-29193634	IMR90	lung:	n/a	n/a
17	POLR2A	chr22:29187650-29192380	U87	brain:	n/a	n/a
18	POLR2A	chr22:29188133-29193629	HepG2	liver:	n/a	n/a
19	POLR2A	chr22:29188548-29193679	GM18951	blood:	n/a	n/a
20	SIN3AK20	chr22:29190921-29193100	MCF-7	breast:	n/a	n/a
21	POLR2A	chr22:29191853-29192512	U87	brain:	n/a	n/a
22	POLR2A	chr22:29186949-29198998	MCF-7	breast:	n/a	n/a
23	POLR2A	chr22:29188054-29192888	MCF10A-Er-Src	breast:	n/a	n/a
24	HEY1	chr22:29190877-29192246	HepG2	liver:	n/a	n/a
25	POLR2A	chr22:29191563-29192231	K562	blood:	n/a	n/a
26	POLR2A	chr22:29189809-29193542	HepG2	liver:	n/a	n/a
27	PML	chr22:29190976-29192300	MCF-7	breast:	n/a	n/a
28	POLR2A	chr22:29191815-29192303	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr22:29191142-29192295	ProgFib	skin:	n/a	n/a
30	POLR2A	chr22:29187041-29192021	MCF10A-Er-Src	breast:	n/a	n/a
31	MBD4	chr22:29189774-29192316	HepG2	liver:	n/a	n/a
32	HEY1	chr22:29188733-29193760	HepG2	liver:	n/a	chr22:29193424-29193433
33	POLR2A	chr22:29191805-29192149	HCT-116	colon:	n/a	n/a
34	POLR2A	chr22:29187961-29193653	GM12891	blood:	n/a	n/a
35	POLR2A	chr22:29191293-29192264	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr22:29189740-29192265	HepG2	liver:	n/a	n/a
37	POLR2A	chr22:29189600-29193715	HepG2	liver:	n/a	n/a
38	POLR2A	chr22:29191853-29192298	U87	brain:	n/a	n/a
39	POLR2A	chr22:29187791-29192417	U87	brain:	n/a	n/a
40	POLR2A	chr22:29188025-29193615	GM18505	blood:	n/a	n/a
41	POLR2A	chr22:29191604-29191934	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr22:29187995-29198706	GM12878	blood:	n/a	n/a
43	POLR2A	chr22:29190892-29192112	GM12892	blood:	n/a	n/a
44	POLR2A	chr22:29188198-29192195	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr22:29189869-29193335	GM12878	blood:	n/a	n/a
46	POLR2A	chr22:29188135-29193499	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29191243..29192935-chr22:29470969..29473140,2	MCF-7	breast:
2	chr22:29190538..29192302-chr22:29232291..29234137,2	MCF-7	breast:
3	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:
4	chr22:29134319..29139472-chr22:29186598..29194420,8	K562	blood:
5	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
6	chr22:29134224..29141746-chr22:29191206..29200044,27	MCF-7	breast:
7	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
8	chr22:29191314..29194018-chr6:26240540..26242629,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226471	TF binding region
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000198327	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12165962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12628211	0.94[ASN][1000 genomes]
rs132531	0.89[JPT][hapmap]
rs132533	0.84[JPT][hapmap]
rs132536	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs132539	0.83[CEU][hapmap]
rs132548	0.89[JPT][hapmap]
rs2064261	0.89[JPT][hapmap]
rs2213645	0.84[JPT][hapmap]
rs2239815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269577	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2881635	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35259224	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs469989	0.87[CEU][hapmap]
rs469990	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs469991	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs4822998	0.82[JPT][hapmap]
rs5752795	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752798	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752801	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752804	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752807	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752813	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762803	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762815	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762824	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762825	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762853	0.83[ASN][1000 genomes]
rs5762854	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5762863	0.83[ASN][1000 genomes]
rs5762864	0.83[ASN][1000 genomes]
rs5762874	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs5762881	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs5762882	0.84[JPT][hapmap]
rs5762936	0.84[JPT][hapmap]
rs5997408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005867	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005869	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005872	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005881	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005892	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005915	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6005916	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005929	0.82[ASN][1000 genomes]
rs6519766	0.89[JPT][hapmap]
rs7287124	0.94[ASN][1000 genomes]
rs7287806	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7287918	0.89[JPT][hapmap]
rs763073	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8137969	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9620841	0.89[JPT][hapmap]
rs9625566	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9625588	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625619	0.80[CEU][hapmap];0.84[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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2097461	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs2097461	CCDC117	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
3	chr22:29187400-29193000	Strong transcription	Fetal Brain Female	brain
4	chr22:29188200-29192200	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr22:29188200-29193000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr22:29188200-29194200	Strong transcription	Brain Cingulate Gyrus	brain
7	chr22:29188400-29193600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr22:29188400-29194200	Strong transcription	Fetal Stomach	stomach
9	chr22:29188600-29192800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr22:29188600-29193200	Strong transcription	Lung	lung
11	chr22:29188600-29194400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:29188800-29192600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr22:29188800-29192800	Strong transcription	NH-A	brain
14	chr22:29188800-29194000	Strong transcription	Fetal Muscle Leg	muscle
15	chr22:29188800-29194200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29188800-29194200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr22:29189000-29194200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr22:29189000-29195000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:29189200-29192800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:29189200-29193400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr22:29189200-29193800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr22:29189200-29194000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr22:29189200-29194000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr22:29189200-29194000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr22:29189200-29194000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr22:29189800-29192400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr22:29189800-29192800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr22:29189800-29193000	Strong transcription	NHLF	lung
29	chr22:29189800-29193200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr22:29189800-29193400	Strong transcription	Brain Hippocampus Middle	brain
31	chr22:29189800-29193600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:29189800-29193600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr22:29189800-29193600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:29189800-29194000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr22:29189800-29194000	Strong transcription	Fetal Lung	lung
36	chr22:29189800-29194000	Strong transcription	HMEC	breast
37	chr22:29189800-29194000	Strong transcription	NHDF-Ad	bronchial
38	chr22:29189800-29194200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr22:29189800-29194600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr22:29189800-29194800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:29190000-29192000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr22:29190000-29192200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr22:29190000-29192600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr22:29190000-29192800	Strong transcription	HSMM	muscle
45	chr22:29190000-29192800	Strong transcription	NHEK	skin
46	chr22:29190000-29193000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:29190000-29193200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr22:29190000-29193200	Strong transcription	Brain Angular Gyrus	brain
49	chr22:29190000-29193200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr22:29190000-29193200	Strong transcription	Fetal Kidney	kidney

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