Variant report

Variant	rs10202550
Chromosome Location	chr2:173418990-173418991
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	GATA2	chr2:173418847-173419870	SH-SY5Y	brain:	n/a	n/a
2	MXI1	chr2:173418707-173422487	SK-N-SH	brain:	n/a	n/a
3	GATA1	chr2:173416948-173422428	PBDE	blood:	n/a	chr2:173421509-173421522
4	POLR2A	chr2:173418889-173421778	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:173411388..173414251-chr2:173417353..173419671,2	K562	blood:
2	chr2:173418979..173421868-chr2:173434562..173438051,3	K562	blood:
3	chr2:173417386..173419457-chr2:173477880..173480867,2	K562	blood:
4	chr2:173416752..173419006-chr2:173419091..173423058,6	K562	blood:
5	chr2:173351396..173353492-chr2:173418976..173421854,2	K562	blood:

Variant related genes	Relation type
PDK1	TF binding region
ENSG00000225205	Chromatin interaction
ENSG00000152256	Chromatin interaction
ENSG00000091409	Chromatin interaction
ENSG00000199866	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10048692	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048707	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048825	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172894	1.00[CHB][hapmap]
rs10176813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181094	1.00[CHB][hapmap]
rs10186869	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197678	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10199472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207262	0.80[ASN][1000 genomes]
rs10208151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427189	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427315	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451559	0.86[CEU][hapmap]
rs10930562	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs11887454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891127	1.00[ASN][1000 genomes]
rs11895461	1.00[CHB][hapmap]
rs11896032	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896178	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897165	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897495	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897582	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898137	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11898890	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901110	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901586	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11902810	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902907	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904366	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693005	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];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693007	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990751	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008835	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009291	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010205	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012115	0.90[CEU][hapmap]
rs13021042	0.89[CEU][hapmap]
rs13023751	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024218	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13024431	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13032610	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032692	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385644	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13386103	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388338	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394924	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398305	0.90[CEU][hapmap]
rs13401945	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13401980	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405998	0.80[ASN][1000 genomes]
rs13408780	0.80[ASN][1000 genomes]
rs13415156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13415174	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425344	0.80[ASN][1000 genomes]
rs1531151	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16860696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740327	0.90[CEU][hapmap]
rs1869922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982410	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290564	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599267	0.80[ASN][1000 genomes]
rs2606069	0.80[ASN][1000 genomes]
rs28537209	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087500	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139806	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34277286	0.81[EUR][1000 genomes]
rs34611798	0.80[ASN][1000 genomes]
rs34707897	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34888332	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35086707	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35156154	0.80[ASN][1000 genomes]
rs35665064	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35809888	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880823	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951155	1.00[ASN][1000 genomes]
rs35999155	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36118221	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3613	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769321	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs3792259	0.90[CEU][hapmap]
rs3816536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59004833	0.87[ASN][1000 genomes]
rs59104969	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62167823	0.80[EUR][1000 genomes]
rs62167832	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169270	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169301	0.80[ASN][1000 genomes]
rs66460331	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710129	0.83[CEU][hapmap]
rs6723872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738196	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs6752257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70937080	0.93[ASN][1000 genomes]
rs7566884	0.93[ASN][1000 genomes]
rs7567092	0.93[ASN][1000 genomes]
rs7596665	0.90[CEU][hapmap]
rs836589	0.80[ASN][1000 genomes]
rs9287957	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10202550	HOXD9	cis	parietal	SCAN
rs10202550	TMPRSS3	trans	lymphoblastoid	seeQTL
rs10202550	LOC440925	cis	parietal	SCAN
rs10202550	ZAK	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173392600-173419600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:173411000-173419600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:173413000-173419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:173413000-173419600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:173413400-173419200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr2:173413800-173419800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr2:173414000-173419400	Weak transcription	Placenta	Placenta
8	chr2:173414600-173419000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:173415000-173419600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr2:173415600-173419200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:173415600-173419200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:173415600-173419400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:173415600-173420000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:173415800-173419200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:173415800-173419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:173415800-173420000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:173416000-173419000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:173416200-173419000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:173416200-173419600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:173416200-173419800	Weak transcription	Right Atrium	heart
21	chr2:173416400-173419000	Weak transcription	HepG2	liver
22	chr2:173416400-173419400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:173416400-173419600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:173416600-173419000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr2:173416600-173419600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr2:173416800-173419200	Weak transcription	Fetal Heart	heart
27	chr2:173417000-173419600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:173417000-173419600	Weak transcription	Adipose Nuclei	Adipose
29	chr2:173417200-173419400	Enhancers	HMEC	breast
30	chr2:173417400-173419600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:173417400-173419600	Enhancers	NHEK	skin
32	chr2:173417400-173419600	Enhancers	NHLF	lung
33	chr2:173417400-173419800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:173417400-173419800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:173417400-173419800	Enhancers	HUVEC	blood vessel
36	chr2:173417400-173420000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:173417600-173419000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:173417600-173419600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:173417800-173419000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:173417800-173419400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:173417800-173419800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:173418200-173419400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:173418200-173419400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:173418200-173419400	Enhancers	Hela-S3	cervix
45	chr2:173418200-173419400	Enhancers	K562	blood
46	chr2:173418200-173419600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:173418200-173419600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:173418200-173419600	Weak transcription	Primary B cells from cord blood	blood
49	chr2:173418200-173419600	Weak transcription	Lung	lung
50	chr2:173418200-173419600	Weak transcription	Osteobl	bone

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