Variant report

Variant	rs7635993
Chromosome Location	chr3:158459976-158459977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158458577..158461138-chr3:158482458..158485038,2	MCF-7	breast:
2	chr3:158459939..158462233-chr3:158502381..158504216,2	K562	blood:
3	chr3:158458014..158460479-chr3:158462665..158465374,2	MCF-7	breast:
4	chr3:158459480..158463209-chr3:158487377..158489850,3	K562	blood:
5	chr3:158450628..158453844-chr3:158458339..158460802,3	MCF-7	breast:
6	chr3:158449518..158452301-chr3:158459445..158461746,2	K562	blood:

Variant related genes	Relation type
ENSG00000118849	Chromatin interaction
ENSG00000240207	Chromatin interaction
ENSG00000118855	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1006911	0.86[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1047366	0.81[YRI][hapmap]
rs12639052	0.81[YRI][hapmap]
rs1346834	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17699456	0.83[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1864507	0.81[YRI][hapmap]
rs1864508	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2115941	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253249	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs2303909	0.82[YRI][hapmap]
rs2364927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2566346	0.87[ASN][1000 genomes]
rs2615052	0.91[ASN][1000 genomes]
rs4680460	0.95[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs4680467	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57932243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61794797	0.85[ASN][1000 genomes]
rs6441224	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6441225	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6772483	0.82[YRI][hapmap]
rs6783879	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs6802315	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6804249	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6804259	0.80[YRI][hapmap]
rs7615751	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618110	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7621897	0.82[YRI][hapmap]
rs8455	0.82[YRI][hapmap]
rs891464	0.82[YRI][hapmap]
rs9819567	0.82[YRI][hapmap]
rs9822005	0.93[ASW][hapmap];0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9825696	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9840571	0.84[CHB][hapmap];0.91[GIH][hapmap];0.84[ASN][1000 genomes]
rs9861938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863103	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866134	0.90[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.85[ASN][1000 genomes]
rs9881462	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7635993	LXN	cis	cerebellum	SCAN
rs7635993	RARRES1	cis	cerebellum	SCAN
rs7635993	MLF1	cis	Heart Left Ventricle	GTEx
rs7635993	TIPARP	cis	cerebellum	SCAN
rs7635993	LXN	cis	parietal	SCAN
rs7635993	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs7635993	GFM1	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450400-158460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
4	chr3:158450800-158460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
8	chr3:158451000-158460000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:158451000-158462000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
13	chr3:158451000-158464400	Weak transcription	NH-A	brain
14	chr3:158451000-158464800	Weak transcription	Gastric	stomach
15	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
17	chr3:158451800-158461400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:158453200-158462000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:158453400-158460800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr3:158453400-158462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
27	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:158453600-158462000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:158453600-158462600	Weak transcription	Brain Substantia Nigra	brain
31	chr3:158453600-158464000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:158453600-158465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
34	chr3:158454000-158460800	Weak transcription	A549	lung
35	chr3:158455400-158465800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:158455800-158460800	Strong transcription	Fetal Stomach	stomach
37	chr3:158456400-158460400	Weak transcription	Placenta	Placenta
38	chr3:158456400-158461600	Weak transcription	Osteobl	bone
39	chr3:158456800-158464800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:158457000-158464600	Weak transcription	HSMM	muscle
41	chr3:158457200-158460200	Weak transcription	Lung	lung
42	chr3:158457200-158464800	Weak transcription	Spleen	Spleen
43	chr3:158457200-158468200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:158457400-158486000	Weak transcription	Right Ventricle	heart
45	chr3:158457800-158460800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:158457800-158464800	Weak transcription	Hela-S3	cervix
47	chr3:158457800-158466000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:158457800-158486200	Weak transcription	Pancreas	Pancrea
49	chr3:158458000-158464800	Weak transcription	HSMMtube	muscle
50	chr3:158458000-158471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links