Variant report

Variant	rs10031989
Chromosome Location	chr4:7797597-7797598
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	chr4:7796049..7798614-chr4:7799200..7800916,2	MCF-7	breast:
2	chr4:7787308..7789396-chr4:7796554..7799014,2	K562	blood:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10000569	0.83[ASN][1000 genomes]
rs10001508	0.86[CEU][hapmap]
rs10004558	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022249	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025396	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050114	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155361	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10937858	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937860	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10937862	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11944501	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501412	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503512	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508657	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12511825	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs16841116	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841207	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429656	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726367	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28735524	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28759100	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689857	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689858	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689861	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4689873	1.00[JPT][hapmap]
rs56919012	0.80[EUR][1000 genomes]
rs6856818	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73206599	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73208810	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356232	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757242	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
10	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
12	chr4:7783400-7798800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:7783400-7799200	Weak transcription	HepG2	liver
14	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
17	chr4:7784200-7797800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:7784200-7800600	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:7784200-7800600	Weak transcription	Esophagus	oesophagus
20	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
21	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:7786000-7800800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:7787200-7799000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:7787400-7800200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:7789400-7799000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr4:7790800-7800800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:7790800-7803600	Strong transcription	HSMM	muscle
32	chr4:7791000-7801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
34	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:7791200-7800800	Weak transcription	Spleen	Spleen
36	chr4:7791400-7800400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:7791600-7797600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:7791600-7799000	Weak transcription	Gastric	stomach
40	chr4:7791600-7799000	Weak transcription	Pancreas	Pancrea
41	chr4:7791600-7800000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:7791600-7800400	Weak transcription	Left Ventricle	heart
43	chr4:7791600-7800400	Weak transcription	Right Ventricle	heart
44	chr4:7791600-7801200	Weak transcription	Fetal Brain Male	brain
45	chr4:7792200-7803200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:7792600-7802800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:7792600-7803400	Strong transcription	A549	lung
48	chr4:7792800-7803000	Strong transcription	HSMMtube	muscle
49	chr4:7793200-7799200	Weak transcription	Primary T cells from cord blood	blood
50	chr4:7793200-7803800	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links