Variant report

Variant	rs2841517
Chromosome Location	chr6:13610188-13610189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13588256..13591251-chr6:13609568..13611670,2	MCF-7	breast:
2	chr6:13606772..13609180-chr6:13609445..13611414,3	K562	blood:
3	chr6:13599146..13601637-chr6:13608396..13610260,2	K562	blood:
4	chr6:13597383..13600646-chr6:13608396..13612792,3	K562	blood:
5	chr6:13572530..13575607-chr6:13609842..13613582,5	K562	blood:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10807467	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10948804	0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10948811	0.92[YRI][hapmap]
rs11962124	0.96[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12209803	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12664567	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1362520	0.82[YRI][hapmap]
rs1573702	0.89[YRI][hapmap]
rs2237092	0.86[YRI][hapmap]
rs2841514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2841515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841518	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841520	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2841521	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2841522	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841523	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841524	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757260	0.96[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3800503	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3823453	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3846912	0.85[YRI][hapmap]
rs3906327	0.89[YRI][hapmap]
rs6459020	0.89[YRI][hapmap]
rs6899402	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6915775	0.82[YRI][hapmap]
rs6940759	0.89[YRI][hapmap]
rs7744218	0.89[YRI][hapmap]
rs7745101	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7760411	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2841517	HIVEP1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13575600-13613800	Weak transcription	Stomach Mucosa	stomach
2	chr6:13575600-13614400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:13575800-13614200	Weak transcription	HUVEC	blood vessel
4	chr6:13575800-13614600	Weak transcription	Right Atrium	heart
5	chr6:13576200-13614400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:13580400-13614800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:13585600-13613800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:13588400-13614200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:13588600-13611800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:13588600-13614000	Weak transcription	NHLF	lung
11	chr6:13588600-13614400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:13588800-13614600	Weak transcription	Small Intestine	intestine
13	chr6:13589000-13611800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:13589000-13614400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:13593000-13613600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:13594400-13613600	Weak transcription	NH-A	brain
17	chr6:13595000-13613600	Weak transcription	Dnd41	blood
18	chr6:13595600-13611800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:13595600-13613200	Weak transcription	Pancreas	Pancrea
20	chr6:13595600-13614600	Weak transcription	Thymus	Thymus
21	chr6:13595600-13614800	Weak transcription	Aorta	Aorta
22	chr6:13595800-13613600	Weak transcription	Fetal Brain Male	brain
23	chr6:13596000-13610800	Weak transcription	GM12878-XiMat	blood
24	chr6:13597200-13613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:13597200-13614400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:13597200-13614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:13597600-13613800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:13597600-13614400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:13597600-13614400	Weak transcription	Fetal Lung	lung
30	chr6:13598200-13613400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:13598600-13613400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:13598600-13614400	Weak transcription	Fetal Kidney	kidney
33	chr6:13599400-13614400	Weak transcription	Esophagus	oesophagus
34	chr6:13599400-13614800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:13599600-13614800	Weak transcription	Gastric	stomach
36	chr6:13601400-13613600	Weak transcription	A549	lung
37	chr6:13601400-13614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:13601400-13614400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:13601600-13613000	Weak transcription	Fetal Brain Female	brain
40	chr6:13601600-13613400	Weak transcription	Brain Anterior Caudate	brain
41	chr6:13601600-13614400	Weak transcription	Colonic Mucosa	Colon
42	chr6:13601600-13614400	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:13601600-13614400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr6:13601600-13614400	Weak transcription	Right Ventricle	heart
45	chr6:13601600-13614400	Weak transcription	Spleen	Spleen
46	chr6:13601600-13614800	Weak transcription	Brain Substantia Nigra	brain
47	chr6:13601800-13611000	Weak transcription	Fetal Heart	heart
48	chr6:13601800-13611800	Weak transcription	Osteobl	bone
49	chr6:13601800-13613600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:13601800-13613600	Weak transcription	NHDF-Ad	bronchial

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