Variant report

Variant	rs35332377
Chromosome Location	chr8:48172962-48172963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:48172645-48173973	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr8:48172708-48173888	GM12892	blood:	n/a	n/a
3	POLR2A	chr8:48172560-48174094	GM12878	blood:	n/a	n/a
4	MAZ	chr8:48172821-48174098	IMR90	lung:	n/a	n/a
5	MAX	chr8:48172936-48174705	NB4	blood:	n/a	n/a
6	YY1	chr8:48172713-48173412	NT2-D1	testis:	n/a	chr8:48173223-48173237 chr8:48173037-48173046 chr8:48173024-48173035 chr8:48172983-48172995
7	POLR2A	chr8:48172954-48174197	HL-60	blood:	n/a	n/a
8	POLR2A	chr8:48172851-48173891	PFSK-1	brain:	n/a	n/a
9	TAF1	chr8:48172867-48173762	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr8:48172931-48173083	K562	blood:	n/a	chr8:48173037-48173046 chr8:48173024-48173035 chr8:48172983-48172995
11	ELF1	chr8:48172643-48174147	GM12878	blood:	n/a	chr8:48172856-48172868 chr8:48173410-48173422
12	POLR2A	chr8:48172858-48173697	GM12878	blood:	n/a	n/a
13	POLR2A	chr8:48172687-48174131	MCF-7	breast:	n/a	n/a
14	POLR2A	chr8:48172613-48173827	K562	blood:	n/a	n/a
15	POLR2A	chr8:48172629-48174164	Raji	blood:	n/a	n/a
16	POLR2A	chr8:48172413-48174341	HepG2	liver:	n/a	n/a
17	RCOR1	chr8:48172892-48174259	K562	blood:	n/a	n/a
18	POLR2A	chr8:48172668-48173799	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr8:48172801-48173192	H1-hESC	embryonic stem cell:	n/a	chr8:48173037-48173046 chr8:48173024-48173035 chr8:48172983-48172995
20	POLR2A	chr8:48172957-48173723	GM12892	blood:	n/a	n/a
21	POLR2A	chr8:48172771-48174007	K562	blood:	n/a	n/a
22	POLR2A	chr8:48172640-48173962	GM18505	blood:	n/a	n/a
23	MAX	chr8:48172943-48174160	GM12878	blood:	n/a	n/a
24	POLR2A	chr8:48172959-48173832	GM18526	blood:	n/a	n/a
25	POLR2A	chr8:48172865-48174146	SK-N-MC	brain:	n/a	n/a
26	RUNX3	chr8:48172911-48173431	GM12878	blood:	n/a	n/a
27	POLR2A	chr8:48172443-48173854	GM12878	blood:	n/a	n/a
28	MAX	chr8:48172885-48173983	A549	lung:	n/a	n/a
29	POLR2A	chr8:48172725-48173944	MCF-7	breast:	n/a	n/a
30	POLR2A	chr8:48172784-48174106	ProgFib	skin:	n/a	n/a
31	POLR2A	chr8:48172961-48173789	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr8:48172953-48173918	GM18951	blood:	n/a	n/a
33	POLR2A	chr8:48172750-48173058	GM12878	blood:	n/a	n/a
34	POLR2A	chr8:48172724-48173848	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr8:48172748-48173812	GM12878	blood:	n/a	n/a
36	MAX	chr8:48172874-48174042	HepG2	liver:	n/a	n/a
37	POLR2A	chr8:48172734-48174123	MCF-7	breast:	n/a	n/a
38	POLR2A	chr8:48172733-48173731	GM12878	blood:	n/a	n/a
39	MTA3	chr8:48172857-48173473	GM12878	blood:	n/a	n/a
40	POLR2A	chr8:48172930-48173821	A549	lung:	n/a	n/a
41	TBP	chr8:48172949-48173580	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr8:48172781-48174097	GM19193	blood:	n/a	n/a
43	CBX3	chr8:48172934-48173548	K562	blood:	n/a	n/a
44	POLR2A	chr8:48172860-48173920	GM12892	blood:	n/a	n/a
45	POLR2A	chr8:48172926-48173024	A549	lung:	n/a	n/a
46	POLR2A	chr8:48172856-48174105	GM12891	blood:	n/a	n/a
47	POLR2A	chr8:48172959-48173889	HUVEC	blood vessel:	n/a	n/a
48	HMGN3	chr8:48172721-48174178	K562	blood:	n/a	n/a
49	HCFC1	chr8:48172784-48174677	Hela-S3	cervix:	n/a	n/a
50	MTA3	chr8:48172836-48173275	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:48105045..48107718-chr8:48171845..48174415,2	MCF-7	breast:
2	chr8:48109425..48112056-chr8:48171977..48173853,2	MCF-7	breast:
3	chr8:48171946..48174429-chr8:48608651..48611565,2	K562	blood:
4	chr8:48171892..48175366-chr8:48649107..48652421,3	K562	blood:
5	chr2:58273888..58274399-chr8:48172813..48173680,2	NB4	blood:
6	chr8:48170516..48173662-chr8:48648596..48652534,4	MCF-7	breast:
7	chr8:48171995..48173689-chr8:48187404..48189747,2	MCF-7	breast:
8	chr8:48171500..48174751-chr8:48648690..48652421,4	K562	blood:
9	chr8:48172897..48175307-chr8:48189146..48191153,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-350F16.2.1-11	chr8:48171254-48173385	NONHSAT126441

No data

Variant related genes	Relation type
SPIDR	TF binding region
ENSG00000028116	Chromatin interaction
ENSG00000164808	Chromatin interaction
ENSG00000253502	Chromatin interaction
ENSG00000253817	Chromatin interaction
ENSG00000221869	Chromatin interaction
ENSG00000248347	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10099236	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10108778	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10441557	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10957370	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11776864	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12547497	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2362555	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28855415	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34506397	0.89[ASN][1000 genomes]
rs4242449	0.91[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4873040	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4873043	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs4873101	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4873269	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58299877	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6420176	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs6473996	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6558201	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs6558202	0.91[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs6981485	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6987882	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6988360	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs6990363	0.87[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs7825148	0.91[EUR][1000 genomes]
rs7828350	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7831310	0.81[EUR][1000 genomes]
rs7832841	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7846620	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025638	chr8:47361534-48176434	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1020467	chr8:47456484-48174712	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv539589	chr8:47456484-48174712	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1028036	chr8:47531749-48256108	Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv1019289	chr8:47536056-48251883	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv539591	chr8:47536056-48251883	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv530882	chr8:47620846-48223868	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv916549	chr8:47982642-48223882	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv1023786	chr8:48163412-48235252	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1031331	chr8:48163412-48239160	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1032993	chr8:48167423-48246277	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1030486	chr8:48167423-48247297	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35332377	SCN1B	trans	parietal	SCAN
rs35332377	MCM4	cis	lymphoblastoid	seeQTL
rs35332377	MCM4	cis	cerebellum	SCAN
rs35332377	KIAA0146	cis	parietal	SCAN
rs35332377	SNAI2	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48168600-48173000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr8:48169400-48173000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:48171800-48174200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr8:48172000-48174400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr8:48172200-48174400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr8:48172400-48173000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:48172400-48173000	Enhancers	Fetal Brain Male	brain
8	chr8:48172400-48174000	Active TSS	Liver	Liver
9	chr8:48172400-48174600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr8:48172600-48173000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:48172600-48173000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:48172600-48173000	Enhancers	Primary B cells from peripheral blood	blood
13	chr8:48172600-48173000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr8:48172600-48173000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:48172600-48173000	Enhancers	Fetal Muscle Leg	muscle
16	chr8:48172600-48173200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr8:48172600-48173200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:48172600-48173400	Flanking Active TSS	Dnd41	blood
19	chr8:48172600-48173400	Flanking Active TSS	GM12878-XiMat	blood
20	chr8:48172600-48173800	Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr8:48172600-48174000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:48172600-48174000	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr8:48172600-48174200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr8:48172600-48174400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr8:48172600-48174400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr8:48172600-48174400	Active TSS	Rectal Smooth Muscle	rectum
27	chr8:48172800-48173000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:48172800-48173000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:48172800-48173000	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr8:48172800-48173000	Enhancers	Primary B cells from cord blood	blood
31	chr8:48172800-48173000	Enhancers	Primary hematopoietic stem cells	blood
32	chr8:48172800-48173000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr8:48172800-48173000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:48172800-48173000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr8:48172800-48173000	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr8:48172800-48173000	Enhancers	Esophagus	oesophagus
37	chr8:48172800-48173000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr8:48172800-48173000	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr8:48172800-48173000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr8:48172800-48173000	Enhancers	Placenta	Placenta
41	chr8:48172800-48173000	Enhancers	Fetal Thymus	thymus
42	chr8:48172800-48173000	Enhancers	Left Ventricle	heart
43	chr8:48172800-48173000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr8:48172800-48173000	Enhancers	Right Atrium	heart
45	chr8:48172800-48173000	Flanking Active TSS	Right Ventricle	heart
46	chr8:48172800-48173000	Enhancers	Stomach Mucosa	stomach
47	chr8:48172800-48173000	Enhancers	Spleen	Spleen
48	chr8:48172800-48173000	Enhancers	HMEC	breast
49	chr8:48172800-48173000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr8:48172800-48173000	Enhancers	NHDF-Ad	bronchial

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