Variant report

Variant	rs4971023
Chromosome Location	chr1:151218894-151218895
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151209513..151214380-chr1:151215209..151220595,6	MCF-7	breast:
2	chr1:151217932..151220850-chr1:151225513..151227250,3	MCF-7	breast:
3	chr1:151215171..151219057-chr1:151223124..151228411,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159352	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1056847	0.95[JPT][hapmap]
rs10749660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10888406	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888408	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888409	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10888410	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11204785	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204791	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204795	0.86[ASN][1000 genomes]
rs11807075	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12022732	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040384	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12048670	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12062719	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12080778	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12407426	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536617	0.86[JPT][hapmap]
rs16827941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833079	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1752387	0.81[JPT][hapmap]
rs1892196	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025900	0.86[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2769268	0.86[JPT][hapmap]
rs2769273	0.86[JPT][hapmap]
rs2800946	0.86[JPT][hapmap]
rs3811405	0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246525	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4291501	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4520422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4522000	0.80[ASN][1000 genomes]
rs4636463	0.85[JPT][hapmap]
rs4970944	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970948	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4971013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971015	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971016	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971025	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971026	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4971029	0.86[JPT][hapmap]
rs4971030	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs5022636	0.86[JPT][hapmap]
rs58323986	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61817972	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587562	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678528	0.91[JPT][hapmap]
rs6681071	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681163	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683396	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6686402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695344	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6701325	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521064	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7527032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545392	0.91[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.90[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:151189600-151223600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:151190400-151223200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:151190400-151223400	Strong transcription	Fetal Thymus	thymus
6	chr1:151191800-151223000	Strong transcription	Fetal Stomach	stomach
7	chr1:151193400-151223000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr1:151194400-151223600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:151195000-151223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:151195200-151227200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:151195600-151223000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:151195600-151223200	Strong transcription	Placenta	Placenta
13	chr1:151196000-151223200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:151196200-151222800	Strong transcription	Thymus	Thymus
15	chr1:151196200-151223200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:151196600-151222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:151196600-151223200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:151196800-151222800	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:151197000-151222800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:151197000-151222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:151197000-151223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:151197200-151223200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:151197400-151223200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:151197400-151223600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:151199200-151222600	Strong transcription	Dnd41	blood
26	chr1:151199200-151223000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:151199400-151222400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:151199400-151222600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:151199400-151222600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:151199400-151223000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:151199400-151223200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:151199600-151222200	Strong transcription	HepG2	liver
33	chr1:151199600-151222400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:151199600-151222400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:151199600-151223200	Strong transcription	Liver	Liver
36	chr1:151199600-151223400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:151199800-151222400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:151199800-151222400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:151199800-151223000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:151199800-151223200	Strong transcription	Adipose Nuclei	Adipose
41	chr1:151201400-151223200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:151202200-151222400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:151202400-151221800	Strong transcription	Hela-S3	cervix
44	chr1:151202400-151222400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:151202400-151223200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:151202400-151223200	Strong transcription	Brain Hippocampus Middle	brain
47	chr1:151202600-151223000	Strong transcription	Primary T cells from cord blood	blood
48	chr1:151202600-151223000	Strong transcription	Colon Smooth Muscle	Colon
49	chr1:151202600-151223000	Strong transcription	Left Ventricle	heart
50	chr1:151202600-151223200	Strong transcription	H9 Cell Line	embryonic stem cell

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