Variant report

Variant	rs4342879
Chromosome Location	chr1:197131655-197131656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197130853..197132396-chr1:197133681..197135184,2	MCF-7	breast:
2	chr1:197121011..197127851-chr1:197128597..197135190,9	K562	blood:
3	chr1:197126302..197127851-chr1:197131460..197133305,2	K562	blood:
4	chr1:197112460..197117731-chr1:197129268..197134426,6	K562	blood:

Variant related genes	Relation type
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1034162	0.81[EUR][1000 genomes]
rs10429911	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs10732295	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10732296	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10733087	0.81[EUR][1000 genomes]
rs10737687	0.85[EUR][1000 genomes]
rs10754213	0.81[EUR][1000 genomes]
rs10754214	0.81[EUR][1000 genomes]
rs10754215	0.81[EUR][1000 genomes]
rs10754219	1.00[CEU][hapmap]
rs10801587	0.81[EUR][1000 genomes]
rs10801588	0.81[EUR][1000 genomes]
rs10801590	0.81[EUR][1000 genomes]
rs10801591	0.81[EUR][1000 genomes]
rs10801593	0.86[AMR][1000 genomes]
rs10801594	0.86[AMR][1000 genomes]
rs10922166	0.81[EUR][1000 genomes]
rs10922169	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1115247	0.87[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs1170880	0.87[CEU][hapmap]
rs1170881	0.87[CEU][hapmap]
rs12092294	0.87[CEU][hapmap]
rs12677	0.87[CEU][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs12731209	0.87[CEU][hapmap]
rs1332662	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs1332663	0.87[CEU][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1412631	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1412632	0.87[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs1412633	0.81[EUR][1000 genomes]
rs1412634	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1415217	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs1537319	0.81[EUR][1000 genomes]
rs1556763	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1571964	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1627765	0.81[EUR][1000 genomes]
rs1759006	0.81[EUR][1000 genomes]
rs1759007	0.81[EUR][1000 genomes]
rs1759008	0.81[EUR][1000 genomes]
rs1759009	0.81[EUR][1000 genomes]
rs1759013	0.81[EUR][1000 genomes]
rs1764800	1.00[CEU][hapmap]
rs1794003	0.81[EUR][1000 genomes]
rs1794010	0.81[EUR][1000 genomes]
rs1888991	0.87[EUR][1000 genomes]
rs1953064	0.81[EUR][1000 genomes]
rs2026429	0.87[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs2151133	0.81[EUR][1000 genomes]
rs2151134	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2151135	0.87[EUR][1000 genomes]
rs3891964	0.81[EUR][1000 genomes]
rs4350226	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4556392	0.87[EUR][1000 genomes]
rs476390	1.00[CEU][hapmap]
rs4915148	0.81[EUR][1000 genomes]
rs4915156	0.81[EUR][1000 genomes]
rs4915313	0.81[EUR][1000 genomes]
rs4915315	0.81[EUR][1000 genomes]
rs4915316	0.81[EUR][1000 genomes]
rs4915327	0.81[EUR][1000 genomes]
rs4915337	0.87[CEU][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs4915345	0.87[EUR][1000 genomes]
rs4915378	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4915379	1.00[CEU][hapmap]
rs5029273	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs510135	1.00[CEU][hapmap]
rs518149	1.00[CEU][hapmap]
rs5997	0.81[EUR][1000 genomes]
rs6003	0.81[EUR][1000 genomes]
rs615647	1.00[CEU][hapmap]
rs616675	1.00[CEU][hapmap]
rs6428387	0.81[EUR][1000 genomes]
rs6428390	0.94[AMR][1000 genomes]
rs6656448	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6656858	0.87[CEU][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6671696	0.81[EUR][1000 genomes]
rs6677082	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs6679189	0.87[EUR][1000 genomes]
rs6680497	0.81[EUR][1000 genomes]
rs6685259	0.81[EUR][1000 genomes]
rs6695300	0.87[EUR][1000 genomes]
rs6701681	0.82[AMR][1000 genomes]
rs6703400	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7411719	0.81[EUR][1000 genomes]
rs7513826	1.00[CEU][hapmap]
rs7516700	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7520503	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs7523013	1.00[CEU][hapmap]
rs7534353	0.87[CEU][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes]
rs7539642	0.81[EUR][1000 genomes]
rs7541429	0.85[EUR][1000 genomes]
rs7542397	0.87[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7554802	0.89[AMR][1000 genomes]
rs7554890	0.86[AMR][1000 genomes]
rs877897	0.87[CEU][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs928439	0.87[CEU][hapmap]
rs928440	0.87[CEU][hapmap]
rs9427660	0.87[CEU][hapmap]
rs9427661	0.87[CEU][hapmap]
rs9427662	0.87[CEU][hapmap]
rs9427942	0.87[CEU][hapmap]
rs9726778	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116400-197132000	Weak transcription	HSMMtube	muscle
2	chr1:197116400-197134800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:197116400-197138800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:197116400-197142200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:197116400-197142200	Weak transcription	HUVEC	blood vessel
6	chr1:197116400-197142400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:197116400-197142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:197116400-197142600	Weak transcription	Fetal Brain Female	brain
9	chr1:197116400-197146200	Weak transcription	Gastric	stomach
10	chr1:197116400-197155000	Weak transcription	Fetal Brain Male	brain
11	chr1:197116600-197135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:197116600-197142600	Weak transcription	HMEC	breast
13	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:197116800-197143200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:197117000-197142600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:197121600-197154800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:197122400-197134800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:197123800-197143200	Weak transcription	Thymus	Thymus
19	chr1:197123800-197147600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:197124200-197136000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:197124200-197140600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:197124200-197143200	Weak transcription	Fetal Heart	heart
23	chr1:197124400-197139600	Weak transcription	GM12878-XiMat	blood
24	chr1:197124600-197142600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:197124600-197155400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:197124800-197139600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:197124800-197144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:197125000-197142400	Weak transcription	Fetal Kidney	kidney
29	chr1:197125200-197141600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:197125200-197142600	Weak transcription	Small Intestine	intestine
31	chr1:197125200-197142800	Weak transcription	NHEK	skin
32	chr1:197125200-197156000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:197125200-197156400	Weak transcription	Right Ventricle	heart
34	chr1:197125400-197155600	Weak transcription	Fetal Stomach	stomach
35	chr1:197125400-197156200	Weak transcription	Pancreas	Pancrea
36	chr1:197125400-197156400	Weak transcription	Aorta	Aorta
37	chr1:197125400-197156400	Weak transcription	Lung	lung
38	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
39	chr1:197125600-197160000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
41	chr1:197125800-197143000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:197125800-197158400	Weak transcription	Spleen	Spleen
43	chr1:197126000-197143000	Weak transcription	Brain Substantia Nigra	brain
44	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:197126800-197132200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:197126800-197132400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:197127000-197132400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:197127000-197148200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:197127400-197132200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:197127400-197132200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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