Variant report

Variant	rs6541360
Chromosome Location	chr1:93823327-93823328
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93816828..93819255-chr1:93822966..93824578,2	MCF-7	breast:

Extended variants
information (count: 143 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10157785	1.00[EUR][1000 genomes]
rs10489733	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1054165	1.00[EUR][1000 genomes]
rs1057256	0.91[AMR][1000 genomes]
rs11164911	1.00[JPT][hapmap]
rs11799543	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11799859	1.00[EUR][1000 genomes]
rs11799928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11800760	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801563	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801977	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11802421	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802822	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11805046	1.00[EUR][1000 genomes]
rs11807404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808266	1.00[EUR][1000 genomes]
rs11808445	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11809153	0.91[AMR][1000 genomes]
rs12239183	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12239921	1.00[EUR][1000 genomes]
rs17109954	1.00[EUR][1000 genomes]
rs17110016	1.00[EUR][1000 genomes]
rs17131715	1.00[EUR][1000 genomes]
rs17131717	1.00[EUR][1000 genomes]
rs1932313	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815413	1.00[JPT][hapmap]
rs28829343	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35555794	1.00[EUR][1000 genomes]
rs41528947	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4847409	1.00[JPT][hapmap]
rs522999	1.00[JPT][hapmap]
rs556888	1.00[JPT][hapmap]
rs55734759	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55738503	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55741554	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55940503	1.00[EUR][1000 genomes]
rs55959166	1.00[EUR][1000 genomes]
rs56281837	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56401576	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56657492	0.82[ASN][1000 genomes]
rs571212	1.00[JPT][hapmap]
rs573056	1.00[JPT][hapmap]
rs57353954	1.00[EUR][1000 genomes]
rs581825	1.00[JPT][hapmap]
rs58351576	1.00[EUR][1000 genomes]
rs58505360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58807475	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59045869	1.00[EUR][1000 genomes]
rs59368083	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59609847	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59774396	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60032869	1.00[EUR][1000 genomes]
rs60046384	1.00[EUR][1000 genomes]
rs60079850	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60497651	0.91[AMR][1000 genomes]
rs60517691	1.00[EUR][1000 genomes]
rs60813039	0.91[AMR][1000 genomes]
rs60868033	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61215181	1.00[EUR][1000 genomes]
rs61252284	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61335636	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61671588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61729705	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs628714	1.00[JPT][hapmap]
rs637198	1.00[JPT][hapmap]
rs6541348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6541378	1.00[EUR][1000 genomes]
rs6541398	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs658877	1.00[JPT][hapmap]
rs6663752	0.84[AMR][1000 genomes]
rs6664053	1.00[EUR][1000 genomes]
rs6664190	0.91[AMR][1000 genomes]
rs6667540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6671070	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6675991	0.91[AMR][1000 genomes]
rs6677114	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6677862	1.00[EUR][1000 genomes]
rs6678465	1.00[EUR][1000 genomes]
rs6679304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6679630	1.00[ASN][1000 genomes]
rs6682265	1.00[EUR][1000 genomes]
rs6687167	1.00[EUR][1000 genomes]
rs6688199	0.91[AMR][1000 genomes]
rs6688513	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs668944	1.00[JPT][hapmap]
rs6691556	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6695142	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6701683	1.00[ASN][1000 genomes]
rs6703963	1.00[EUR][1000 genomes]
rs6704067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72955374	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72955379	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72955402	0.91[AMR][1000 genomes]
rs72957210	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72957220	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72957300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72959204	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72959216	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959225	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959236	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959238	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959240	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959245	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72959255	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959260	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959267	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72959273	1.00[ASN][1000 genomes]
rs72961310	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72961322	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72961328	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74101439	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101447	1.00[EUR][1000 genomes]
rs74101453	1.00[EUR][1000 genomes]
rs74101458	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74101464	1.00[EUR][1000 genomes]
rs74101470	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74101603	1.00[EUR][1000 genomes]
rs74104014	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs74104033	1.00[EUR][1000 genomes]
rs7512471	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7518171	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518930	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7519163	1.00[JPT][hapmap]
rs7525388	1.00[EUR][1000 genomes]
rs7527459	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7529230	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7530923	1.00[EUR][1000 genomes]
rs7533526	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7537939	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7540960	1.00[ASN][1000 genomes]
rs7544352	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7545154	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7545358	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548629	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs754899	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8489	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8561	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9324347	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9659202	0.91[AMR][1000 genomes]
rs9662414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93812800-93823800	Weak transcription	Spleen	Spleen
2	chr1:93812800-93831000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93812800-93832200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:93813000-93823800	Weak transcription	Gastric	stomach
5	chr1:93813400-93840000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:93813400-93840400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:93814200-93823600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:93814200-93823800	Weak transcription	Right Ventricle	heart
9	chr1:93815400-93839800	Weak transcription	Aorta	Aorta
10	chr1:93815600-93834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:93816000-93823800	Weak transcription	Stomach Mucosa	stomach
12	chr1:93816000-93832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:93816200-93823400	Weak transcription	HSMMtube	muscle
14	chr1:93816600-93841800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:93816800-93841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:93817400-93823400	Weak transcription	Lung	lung
17	chr1:93817600-93823800	Weak transcription	Fetal Brain Female	brain
18	chr1:93817600-93824600	Strong transcription	Fetal Intestine Large	intestine
19	chr1:93817800-93832400	Weak transcription	Psoas Muscle	Psoas
20	chr1:93818000-93826400	Strong transcription	Placenta	Placenta
21	chr1:93818000-93835400	Weak transcription	Small Intestine	intestine
22	chr1:93818200-93823600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:93818200-93823600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:93818200-93823800	Weak transcription	Pancreas	Pancrea
25	chr1:93818200-93826400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:93818200-93826600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:93818400-93823600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:93818400-93823600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:93818400-93823800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:93818400-93824200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:93818400-93824400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:93818400-93825600	Strong transcription	Primary B cells from cord blood	blood
33	chr1:93818400-93826200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:93818400-93836000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:93818600-93823600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:93818600-93823600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:93818600-93823600	Weak transcription	Fetal Heart	heart
38	chr1:93818600-93824600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr1:93818800-93827200	Strong transcription	Fetal Thymus	thymus
40	chr1:93818800-93837200	Weak transcription	Fetal Kidney	kidney
41	chr1:93819000-93823600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:93819000-93828000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:93819000-93833200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:93819200-93823800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:93819200-93823800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:93819200-93824800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:93819200-93826400	Strong transcription	HUVEC	blood vessel
48	chr1:93819400-93826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:93819400-93832000	Strong transcription	HSMM	muscle
50	chr1:93819400-93834600	Strong transcription	Primary B cells from peripheral blood	blood

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