Variant report

Variant	rs3006436
Chromosome Location	chr1:153438422-153438423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153437926..153438880-chr1:153467491..153468041,2	MCF-7	breast:
2	chr1:153372721..153373690-chr1:153438049..153438638,2	MCF-7	breast:
3	chr1:153436847..153439085-chr1:153446138..153447980,2	MCF-7	breast:
4	chr1:153437206..153440694-chr1:153466029..153468031,4	MCF-7	breast:
5	chr1:153438181..153439098-chr1:153467083..153468312,5	MCF-7	breast:
6	chr1:153327533..153328170-chr1:153438174..153438874,2	MCF-7	breast:
7	chr1:153321143..153321972-chr1:153438103..153438851,2	MCF-7	breast:
8	chr1:153437921..153438982-chr1:153467024..153468074,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-S100A7A-1	chr1:153433284-153441910	predAs_engstrom06_BM723462_1

No data

Variant related genes	Relation type
ENSG00000163218	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1024274	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888561	0.80[ASN][1000 genomes]
rs10888563	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888564	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888565	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888566	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11205301	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145434	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1326290	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1409366	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555885	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026604	0.81[ASN][1000 genomes]
rs2038927	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2038928	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2148713	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2986208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2986213	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3006435	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4240869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4590630	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845349	0.81[ASN][1000 genomes]
rs4845546	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6421468	0.85[ASN][1000 genomes]
rs6587740	0.81[ASN][1000 genomes]
rs6657653	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698784	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs715754	0.84[ASN][1000 genomes]
rs715755	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7512616	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7535089	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs913057	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs983844	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153431000-153439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153435800-153439200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:153438000-153438600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr1:153438000-153438600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr1:153438000-153439000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:153438000-153439600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:153438000-153440000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:153438000-153441000	Enhancers	Fetal Heart	heart
9	chr1:153438200-153438600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr1:153438200-153438600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:153438200-153438600	Enhancers	Liver	Liver
12	chr1:153438200-153438600	Enhancers	Fetal Muscle Trunk	muscle
13	chr1:153438200-153438600	Enhancers	K562	blood
14	chr1:153438200-153438800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr1:153438200-153438800	Enhancers	Small Intestine	intestine
16	chr1:153438200-153439000	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr1:153438200-153439400	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr1:153438200-153439600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:153438200-153439600	Enhancers	Ovary	ovary
20	chr1:153438200-153439600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:153438200-153439600	Enhancers	NHLF	lung
22	chr1:153438200-153439800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:153438200-153439800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:153438200-153439800	Enhancers	Fetal Lung	lung
25	chr1:153438400-153438600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:153438400-153438600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:153438400-153438600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
28	chr1:153438400-153438600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:153438400-153438600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr1:153438400-153438600	Enhancers	HMEC	breast
31	chr1:153438400-153438600	Flanking Active TSS	NHEK	skin
32	chr1:153438400-153438800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:153438400-153438800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:153438400-153438800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:153438400-153438800	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr1:153438400-153439000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:153438400-153439000	Enhancers	Esophagus	oesophagus
38	chr1:153438400-153439000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr1:153438400-153439000	Bivalent Enhancer	Fetal Stomach	stomach
40	chr1:153438400-153439000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:153438400-153439400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:153438400-153439400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:153438400-153439600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr1:153438400-153440000	Enhancers	Left Ventricle	heart
45	chr1:153438400-153440000	Enhancers	NH-A	brain

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