Variant report

Variant	rs34213500
Chromosome Location	chr19:18524488-18524489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:18524380-18524530	AG04449	skin:	n/a	n/a
2	CTCF	chr19:18524340-18524490	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr19:18524380-18524530	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr19:18524340-18524490	WERI-Rb-1	eye:	n/a	n/a
5	CTCF	chr19:18524340-18524490	HEK293	kidney:	n/a	n/a
6	CTCF	chr19:18524400-18524550	BJ	skin:	n/a	n/a
7	CTCF	chr19:18524340-18524490	NB4	blood:	n/a	n/a
8	CTCF	chr19:18524380-18524530	GM12878	blood:	n/a	n/a
9	CTCF	chr19:18524380-18524530	HepG2	liver:	n/a	n/a
10	CTCF	chr19:18524440-18524590	RPTEC	kidney:	n/a	n/a
11	CTCF	chr19:18524360-18524510	HRPEpiC	eye:	n/a	n/a
12	CTCF	chr19:18524340-18524490	HRE	kidney:	n/a	n/a
13	CTCF	chr19:18524360-18524510	AG09319	gingival:	n/a	n/a
14	CTCF	chr19:18524400-18524550	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18385043..18394940-chr19:18518893..18533267,53	K562	blood:
2	chr19:18333703..18336599-chr19:18524425..18529905,5	K562	blood:
3	chr19:18520199..18523408-chr19:18523976..18531789,10	MCF-7	breast:
4	chr19:18320883..18322593-chr19:18524287..18527226,2	K562	blood:
5	chr19:18450116..18452798-chr19:18524021..18525945,2	MCF-7	breast:
6	chr19:18399894..18406849-chr19:18524216..18528146,7	K562	blood:
7	chr19:18508054..18515743-chr19:18523957..18529414,9	K562	blood:
8	chr19:18523615..18525395-chr19:18528501..18530653,2	MCF-7	breast:
9	chr19:18448952..18453435-chr19:18523841..18530143,7	K562	blood:
10	chr19:18340431..18343253-chr19:18523946..18525951,2	K562	blood:
11	chr19:18458615..18460578-chr19:18524334..18527055,2	MCF-7	breast:
12	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
13	chr19:18495627..18501937-chr19:18519170..18524838,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000221167	TF binding region
ENSG00000267959	Chromatin interaction
ENSG00000241464	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000105650	Chromatin interaction
ENSG00000130518	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000175489	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000221167	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10402247	0.86[EUR][1000 genomes]
rs10402322	0.81[ASN][1000 genomes]
rs10409346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10409408	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10410797	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10416993	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10418554	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10420384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10423802	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10426768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1045631	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11086110	0.81[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668704	0.85[ASN][1000 genomes]
rs11670392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11672385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11879757	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12980726	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12982295	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12983263	0.84[EUR][1000 genomes]
rs13344313	0.88[CHD][hapmap]
rs1469412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1469413	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1971093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2013069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2162797	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303692	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28534973	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2891676	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35004712	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35336015	0.86[EUR][1000 genomes]
rs35742476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4006662	0.81[EUR][1000 genomes]
rs4303657	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4580317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4808135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4808802	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808803	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808805	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808808	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4808811	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4808812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55715336	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57923655	0.81[EUR][1000 genomes]
rs6512268	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6512269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6512270	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6512271	0.82[ASN][1000 genomes]
rs7246788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247540	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7249760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.81[EUR][1000 genomes]
rs7252185	0.81[EUR][1000 genomes]
rs7255936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256530	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7258891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259135	0.83[ASN][1000 genomes]
rs7507218	0.80[EUR][1000 genomes]
rs8100343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102717	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8104247	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs8106332	0.81[EUR][1000 genomes]
rs8111397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111582	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112372	0.81[EUR][1000 genomes]
rs8112859	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs888668	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs888669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
9	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv911277	chr19:18520231-18552139	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs34213500	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs34213500	CHERP	cis	cerebellum	SCAN
rs34213500	SSBP4	cis	lymphoblastoid	seeQTL
rs34213500	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs34213500	ABHD8	cis	parietal	SCAN
rs34213500	SSBP4	cis	cerebellum	SCAN
rs34213500	ZNF14	cis	parietal	SCAN
rs34213500	F2RL3	cis	cerebellum	SCAN
rs34213500	ISYNA1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18508400-18525400	Weak transcription	Right Atrium	heart
2	chr19:18508800-18525200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr19:18513000-18525600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:18515200-18524800	Weak transcription	A549	lung
5	chr19:18515200-18524800	Weak transcription	HepG2	liver
6	chr19:18515200-18525000	Weak transcription	Fetal Intestine Large	intestine
7	chr19:18516200-18524800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:18519200-18524800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr19:18519200-18524800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:18519400-18525200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr19:18519600-18524800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:18519800-18525000	Weak transcription	GM12878-XiMat	blood
13	chr19:18520400-18525200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:18520600-18525200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:18521600-18524800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:18521600-18524800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr19:18521600-18525000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:18521600-18525000	Weak transcription	Fetal Stomach	stomach
19	chr19:18521600-18525000	Weak transcription	NHLF	lung
20	chr19:18521600-18525000	Weak transcription	Osteobl	bone
21	chr19:18521600-18525200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:18521600-18525200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:18521600-18525200	Weak transcription	Fetal Kidney	kidney
24	chr19:18521600-18525200	Weak transcription	Hela-S3	cervix
25	chr19:18521600-18525400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:18521600-18525400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:18521600-18526400	Weak transcription	Pancreas	Pancrea
28	chr19:18521600-18527400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:18521800-18524800	Weak transcription	Dnd41	blood
30	chr19:18521800-18524800	Weak transcription	K562	blood
31	chr19:18521800-18525000	Weak transcription	Liver	Liver
32	chr19:18521800-18525000	Weak transcription	Ovary	ovary
33	chr19:18521800-18525200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr19:18522000-18524800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:18523600-18525000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr19:18523600-18525200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:18523800-18524800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:18523800-18525000	Weak transcription	Fetal Intestine Small	intestine
39	chr19:18524000-18525000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:18524200-18525800	Enhancers	Brain Germinal Matrix	brain

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