Variant report

Variant	rs7600550
Chromosome Location	chr2:114484421-114484422
allele	C/T
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	chr2:114484322-114484602	K562	blood:	n/a	n/a
2	POLR2A	chr2:114484118-114484540	K562	blood:	n/a	n/a
3	POLR2A	chr2:114484261-114484691	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:114484206-114484432	K562	blood:	n/a	n/a
5	POLR2A	chr2:114484097-114484474	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:114484161-114484476	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114476035..114479420-chr2:114481411..114484659,3	K562	blood:
2	chr2:114482332..114485532-chr2:114485677..114488517,3	K562	blood:

Variant related genes	Relation type
SLC35F5	TF binding region
ENSG00000265429	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10168234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200355	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10205467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678202	0.81[CHB][hapmap]
rs11679707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682259	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688799	0.80[ASN][1000 genomes]
rs11695798	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11897553	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11901060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711786	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006627	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13029093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034531	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13397540	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13405475	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13416930	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1349157	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1584434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17048473	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2122095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs35432356	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35667749	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849264	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849265	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849266	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4849269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849274	0.82[JPT][hapmap]
rs56213422	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56376185	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58473055	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542171	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6709158	0.84[CHB][hapmap]
rs6726001	0.84[CHB][hapmap]
rs6731402	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6741521	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67850681	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561176	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7578249	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586800	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7590375	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7592689	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935644	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9798411	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7600550	DDX11L2	cis	Whole Blood	GTEx
rs7600550	RPL23AP7	cis	Muscle Skeletal	GTEx
rs7600550	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs7600550	RPL23AP7	cis	Whole Blood	GTEx
rs7600550	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx
rs7600550	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs7600550	SLC35F5	cis	parietal	SCAN
rs7600550	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs7600550	IL1B	cis	cerebellum	SCAN
rs7600550	SLC35F5	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114486200	Weak transcription	Dnd41	blood
2	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
6	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
7	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
8	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
9	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
10	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
11	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
14	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
17	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:114469800-114486400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:114470000-114497400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:114470000-114500200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:114470200-114493400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:114470400-114510800	Strong transcription	HSMM	muscle
25	chr2:114471000-114486000	Weak transcription	K562	blood
26	chr2:114471000-114488200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:114471000-114495600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:114471000-114495600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:114471000-114498600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:114471000-114500200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:114472800-114486200	Weak transcription	A549	lung
32	chr2:114472800-114486600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:114473200-114488600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:114473200-114494600	Weak transcription	Fetal Heart	heart
35	chr2:114473400-114484800	Weak transcription	HMEC	breast
36	chr2:114473800-114497200	Weak transcription	NHEK	skin
37	chr2:114474400-114486000	Weak transcription	GM12878-XiMat	blood
38	chr2:114474400-114494600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:114474400-114507600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:114475200-114486400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:114475600-114486200	Weak transcription	Brain Substantia Nigra	brain
42	chr2:114475600-114486800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:114476000-114506600	Weak transcription	Thymus	Thymus
44	chr2:114476800-114484600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:114477000-114484600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:114477200-114488200	Weak transcription	NH-A	brain
47	chr2:114478800-114486400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:114478800-114487200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:114478800-114504400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:114478800-114507600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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