Variant report

Variant	rs12197259
Chromosome Location	chr6:53596974-53596975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53587433..53591147-chr6:53595586..53599292,4	MCF-7	breast:
2	chr6:53595711..53597938-chr6:53598268..53600839,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10456164	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10456671	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193312	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13191282	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13195168	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13196802	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13206978	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13211007	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13219456	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000995	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003502	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4302662	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4409173	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4416674	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4428502	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4443499	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4469293	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4479931	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555913	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4574642	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4715423	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458955	0.85[EUR][1000 genomes]
rs6909833	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930030	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930035	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7755196	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755522	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7773640	0.87[CEU][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12197259	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs12197259	KLHL31	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53589800-53599400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53591000-53599000	Weak transcription	Stomach Mucosa	stomach
3	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:53593000-53599800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:53593600-53598400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:53593600-53598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:53593600-53598600	Weak transcription	Fetal Intestine Large	intestine
10	chr6:53593600-53599000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:53593600-53599200	Weak transcription	NH-A	brain
12	chr6:53593600-53599400	Enhancers	Hela-S3	cervix
13	chr6:53593600-53599400	Weak transcription	HSMMtube	muscle
14	chr6:53593600-53599800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:53593600-53600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:53593800-53597200	Weak transcription	NHEK	skin
17	chr6:53593800-53598400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:53593800-53598400	Weak transcription	HMEC	breast
19	chr6:53593800-53598600	Weak transcription	A549	lung
20	chr6:53593800-53599200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:53593800-53599800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:53594600-53599600	Weak transcription	Placenta	Placenta
23	chr6:53595000-53599800	Enhancers	Dnd41	blood
24	chr6:53595200-53597200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:53595200-53597400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:53595400-53599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:53595800-53599200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:53596000-53599400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:53596000-53599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:53596000-53599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:53596000-53601600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:53596200-53597800	Enhancers	Fetal Thymus	thymus
34	chr6:53596400-53597200	Enhancers	Ovary	ovary
35	chr6:53596600-53597200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:53596600-53597400	Enhancers	Primary T cells from cord blood	blood
37	chr6:53596600-53597400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:53596600-53597400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:53596600-53597800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:53596600-53597800	Enhancers	Thymus	Thymus
41	chr6:53596800-53597000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr6:53596800-53597200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:53596800-53597200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr6:53596800-53597200	Enhancers	HUVEC	blood vessel
45	chr6:53596800-53597400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:53596800-53597400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:53596800-53597400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:53596800-53597600	Enhancers	Fetal Brain Male	brain

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