Variant report

Variant	rs2405442
Chromosome Location	chr7:99971313-99971314
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	chr7:99968973-99971363	HL-60	blood:	n/a	n/a
2	POLR2A	chr7:99971302-99971684	HepG2	liver:	n/a	n/a
3	CTCF	chr7:99971280-99971430	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:99967786-99971318	A549	lung:	n/a	n/a
5	POLR2A	chr7:99969922-99971920	K562	blood:	n/a	n/a
6	POLR2A	chr7:99968372-99971597	K562	blood:	n/a	n/a
7	POLR2A	chr7:99971076-99971336	GM12878	blood:	n/a	n/a
8	CTCF	chr7:99971310-99971418	GM19238	blood:	n/a	n/a
9	CTCF	chr7:99971300-99971450	GM12865	blood:	n/a	n/a
10	MTA3	chr7:99971307-99972082	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:99971210-99971345	HepG2	liver:	n/a	n/a
12	SPI1	chr7:99970822-99971376	HL-60	blood:	n/a	n/a
13	CTCF	chr7:99971300-99971450	GM12872	blood:	n/a	n/a
14	POLR2A	chr7:99967810-99971498	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:2254016..2256891-chr7:99969269..99971399,2	MCF-7	breast:
2	chr7:99752659..99755597-chr7:99969374..99971671,2	K562	blood:

Variant related genes	Relation type
PILRA	TF binding region
ENSG00000146826	Chromatin interaction
ENSG00000252958	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000167965	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1043915	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1061230	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs10953295	0.82[CHB][hapmap]
rs1138417	0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs11764176	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs12539172	1.00[ASW][hapmap];0.81[YRI][hapmap]
rs12666425	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12705073	0.82[CHB][hapmap]
rs1476679	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs1623264	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1624099	0.82[CHB][hapmap]
rs1636975	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1637001	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs1727128	0.87[CHB][hapmap]
rs1727133	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs1727134	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1727138	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs1727140	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1859788	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246713	0.82[CHB][hapmap]
rs2528900	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2734897	0.87[YRI][hapmap]
rs2906646	0.82[CHB][hapmap]
rs2950518	0.82[CHB][hapmap]
rs2950520	1.00[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs34919929	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs34995835	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs3735241	0.82[CHB][hapmap]
rs3735242	0.82[CHB][hapmap]
rs3779045	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6948729	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs705867	0.82[CHB][hapmap]
rs7384878	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7794170	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7811662	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs858506	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs858513	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs866500	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs941287	0.82[CHB][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	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2405442	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2405442	PILRB	cis	Adipose Subcutaneous	GTEx
rs2405442	GATS	cis	lymphoblastoid	seeQTL
rs2405442	PVRIG2P	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99934000-99977600	Weak transcription	Fetal Brain Male	brain
2	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
3	chr7:99960200-99975400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:99960400-99984800	Weak transcription	Pancreas	Pancrea
5	chr7:99960600-99975600	Weak transcription	Brain Angular Gyrus	brain
6	chr7:99960600-99977600	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:99960600-99985200	Weak transcription	Aorta	Aorta
8	chr7:99960800-99971800	Weak transcription	HSMMtube	muscle
9	chr7:99960800-99976600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:99961400-99977400	Weak transcription	Brain Substantia Nigra	brain
11	chr7:99962400-100020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:99962800-99972800	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:99963000-99971400	Enhancers	Primary B cells from cord blood	blood
14	chr7:99964800-99977600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:99965200-99976800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:99965200-99979200	Weak transcription	Right Ventricle	heart
17	chr7:99966000-99971400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:99966000-99974000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:99966400-99998000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:99966600-99972000	Weak transcription	Liver	Liver
21	chr7:99966600-99972800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:99966600-99973600	Weak transcription	Ovary	ovary
23	chr7:99966800-99972600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr7:99967000-99971400	Enhancers	Placenta	Placenta
25	chr7:99967000-99972200	Weak transcription	Thymus	Thymus
26	chr7:99967200-99971400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:99967200-99971800	Weak transcription	K562	blood
28	chr7:99967400-99974600	Weak transcription	Fetal Brain Female	brain
29	chr7:99967800-99971400	Enhancers	Adipose Nuclei	Adipose
30	chr7:99968400-99971600	Enhancers	Fetal Muscle Trunk	muscle
31	chr7:99969200-99971400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:99969200-99972000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr7:99969200-99973000	Enhancers	Fetal Thymus	thymus
34	chr7:99969400-99971400	Enhancers	Fetal Muscle Leg	muscle
35	chr7:99969400-99971800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:99969400-99982600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:99969600-99971400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:99969600-99971600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:99969600-99972000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:99969800-99977000	Weak transcription	Brain Germinal Matrix	brain
41	chr7:99970000-99971800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr7:99970000-99971800	Enhancers	GM12878-XiMat	blood
43	chr7:99970000-99972400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:99970000-99972400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr7:99970200-99971400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:99970200-99971400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr7:99970200-99973000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr7:99970200-99978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:99970400-99972000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:99970400-99972400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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