Variant report

Variant	rs226424
Chromosome Location	chr17:34055643-34055644
allele	G/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	chr17:34053798-34057239	K562	blood:	n/a	n/a
2	POLR2A	chr17:34055493-34055930	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr17:34054107-34057401	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr17:34055441-34055713	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:34055640-34055934	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:34055553-34055906	K562	blood:	n/a	n/a
7	POLR2A	chr17:34055404-34055686	K562	blood:	n/a	n/a
8	POLR2A	chr17:34055304-34056986	A549	lung:	n/a	n/a
9	POLR2A	chr17:34055537-34056006	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34048477..34051803-chr17:34054688..34058128,3	K562	blood:
2	chr17:34053645..34055834-chr17:34135102..34137667,2	MCF-7	breast:

Variant related genes	Relation type
RASL10B	TF binding region
ENSG00000267578	Chromatin interaction
ENSG00000172660	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1037591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10491114	0.86[ASW][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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs10491115	0.87[EUR][1000 genomes]
rs12449919	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12450039	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12452633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12600662	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12603142	0.87[EUR][1000 genomes]
rs16971122	0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2079924	0.86[EUR][1000 genomes]
rs226427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs226433	0.86[ASW][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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs226435	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs226436	1.00[ASW][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];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs226437	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278950	1.00[ASW][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];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2428463	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523115	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28384428	0.86[ASW][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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs28661650	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3760325	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3785759	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3785763	0.87[EUR][1000 genomes]
rs7213022	0.91[AFR][1000 genomes]
rs9303689	0.86[ASW][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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9904644	1.00[ASW][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs9907911	1.00[YRI][hapmap]
rs9914730	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9916483	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:34024200-34056200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:34032600-34055800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr17:34035400-34056200	Strong transcription	A549	lung
5	chr17:34036600-34055800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:34044800-34055800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:34045000-34058000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr17:34046600-34056200	Strong transcription	HMEC	breast
9	chr17:34050200-34055800	Strong transcription	Thymus	Thymus
10	chr17:34050400-34056000	Strong transcription	Lung	lung
11	chr17:34052200-34057800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:34052400-34057600	Weak transcription	Brain Substantia Nigra	brain
13	chr17:34052600-34058600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr17:34052800-34056600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:34052800-34057600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:34052800-34057800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:34052800-34058000	Weak transcription	Fetal Brain Male	brain
18	chr17:34052800-34058200	Weak transcription	Aorta	Aorta
19	chr17:34053000-34057600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:34053000-34057800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:34053000-34058200	Weak transcription	Colonic Mucosa	Colon
22	chr17:34053000-34058200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr17:34053000-34058200	Weak transcription	K562	blood
24	chr17:34053200-34056000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:34053200-34056200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr17:34053200-34056600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr17:34053200-34057600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr17:34053200-34057600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr17:34053200-34057600	Weak transcription	Brain Hippocampus Middle	brain
30	chr17:34053200-34057600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:34053200-34057800	Weak transcription	Brain Germinal Matrix	brain
32	chr17:34053200-34057800	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:34053200-34057800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:34053400-34055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr17:34053600-34057800	Weak transcription	NHEK	skin
36	chr17:34053800-34056000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr17:34053800-34056200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:34053800-34056200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:34054200-34056200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr17:34054200-34057600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr17:34054200-34057600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr17:34054200-34057600	Weak transcription	Right Ventricle	heart
43	chr17:34054200-34057600	Weak transcription	HepG2	liver
44	chr17:34054200-34058000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:34054200-34058000	Weak transcription	HSMM	muscle
46	chr17:34054200-34058200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:34054400-34056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr17:34054400-34056200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr17:34054400-34056800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:34054400-34057600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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